Starting phenix.real_space_refine on Tue Nov 19 00:44:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/11_2024/6rqh_4982.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 236 5.16 5 C 32076 2.51 5 N 8779 2.21 5 O 9683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50851 Number of models: 1 Model: "" Number of chains: 20 Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 779 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 817 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "Q" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3675 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 422} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "M" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 11836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1518, 11836 Classifications: {'peptide': 1518} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 62, 'TRANS': 1455} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3807 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb=" P DG U 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG U 12 " occ=0.00 residue: pdb=" P DA U 19 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 19 " occ=0.00 residue: pdb=" P DA U 31 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 31 " occ=0.00 Time building chain proxies: 25.31, per 1000 atoms: 0.50 Number of scatterers: 50851 At special positions: 0 Unit cell: (159.273, 222.774, 191.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 77 15.00 O 9683 8.00 N 8779 7.00 C 32076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 233 " distance=2.03 Simple disulfide: pdb=" SG CYS I 13 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 10 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.80 Conformation dependent library (CDL) restraints added in 5.9 seconds 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11674 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 0 sheets defined 35.4% alpha, 0.0% beta 4 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 14.22 Creating SS restraints... Processing helix chain 'Q' and resid 98 through 122 removed outlier: 3.595A pdb=" N PHE Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU Q 105 " --> pdb=" O LYS Q 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE Q 108 " --> pdb=" O PHE Q 104 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU Q 112 " --> pdb=" O PHE Q 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 130 Processing helix chain 'Q' and resid 131 through 133 No H-bonds generated for 'chain 'Q' and resid 131 through 133' Processing helix chain 'Q' and resid 134 through 139 Processing helix chain 'Q' and resid 140 through 146 removed outlier: 3.737A pdb=" N ILE Q 144 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 3.517A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 183 Processing helix chain 'Q' and resid 211 through 216 removed outlier: 3.707A pdb=" N GLU Q 216 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 removed outlier: 3.506A pdb=" N LYS Q 229 " --> pdb=" O GLN Q 225 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE Q 230 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 225 through 230' Processing helix chain 'Q' and resid 231 through 233 No H-bonds generated for 'chain 'Q' and resid 231 through 233' Processing helix chain 'Q' and resid 238 through 243 removed outlier: 3.842A pdb=" N PHE Q 242 " --> pdb=" O HIS Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 260 removed outlier: 4.054A pdb=" N LEU Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU Q 253 " --> pdb=" O CYS Q 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 270 removed outlier: 4.165A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR Q 270 " --> pdb=" O PHE Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 275 removed outlier: 3.616A pdb=" N GLU Q 275 " --> pdb=" O LYS Q 271 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 317 removed outlier: 3.625A pdb=" N VAL Q 306 " --> pdb=" O ALA Q 302 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE Q 310 " --> pdb=" O VAL Q 306 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET Q 311 " --> pdb=" O LEU Q 307 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU Q 312 " --> pdb=" O SER Q 308 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR Q 313 " --> pdb=" O TYR Q 309 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 331 through 336 removed outlier: 3.876A pdb=" N THR Q 335 " --> pdb=" O ILE Q 331 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU Q 336 " --> pdb=" O LEU Q 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 331 through 336' Processing helix chain 'Q' and resid 346 through 357 removed outlier: 3.702A pdb=" N ASN Q 351 " --> pdb=" O SER Q 347 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE Q 352 " --> pdb=" O ILE Q 348 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Q 354 " --> pdb=" O ARG Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 369 removed outlier: 3.961A pdb=" N GLN Q 368 " --> pdb=" O ASP Q 365 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP Q 369 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 365 through 369' Processing helix chain 'Q' and resid 370 through 385 removed outlier: 3.580A pdb=" N PHE Q 377 " --> pdb=" O GLU Q 373 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU Q 382 " --> pdb=" O LEU Q 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 417 Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.749A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG Q 445 " --> pdb=" O ASP Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 470 through 490 removed outlier: 4.097A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG Q 478 " --> pdb=" O GLU Q 474 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU Q 479 " --> pdb=" O ALA Q 475 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA Q 484 " --> pdb=" O LEU Q 480 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER Q 485 " --> pdb=" O THR Q 481 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU Q 488 " --> pdb=" O ALA Q 484 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL Q 489 " --> pdb=" O SER Q 485 " (cutoff:3.500A) Processing helix chain 'Q' and resid 495 through 503 removed outlier: 3.617A pdb=" N ASP Q 500 " --> pdb=" O GLU Q 496 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) Processing helix chain 'Q' and resid 505 through 513 Processing helix chain 'S' and resid 190 through 194 removed outlier: 3.855A pdb=" N LEU S 193 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG S 194 " --> pdb=" O SER S 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 190 through 194' Processing helix chain 'S' and resid 571 through 576 removed outlier: 4.248A pdb=" N ALA S 575 " --> pdb=" O HIS S 571 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER S 576 " --> pdb=" O PRO S 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 571 through 576' Processing helix chain 'S' and resid 585 through 601 removed outlier: 4.226A pdb=" N ILE S 589 " --> pdb=" O GLU S 585 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER S 594 " --> pdb=" O GLY S 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS S 597 " --> pdb=" O VAL S 593 " (cutoff:3.500A) Processing helix chain 'S' and resid 602 through 604 No H-bonds generated for 'chain 'S' and resid 602 through 604' Processing helix chain 'S' and resid 605 through 613 Processing helix chain 'S' and resid 616 through 629 removed outlier: 4.242A pdb=" N TYR S 622 " --> pdb=" O ASP S 618 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN S 624 " --> pdb=" O ASP S 620 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP S 625 " --> pdb=" O LYS S 621 " (cutoff:3.500A) Processing helix chain 'S' and resid 634 through 639 Processing helix chain 'S' and resid 671 through 686 removed outlier: 3.885A pdb=" N PHE S 675 " --> pdb=" O SER S 671 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER S 676 " --> pdb=" O ILE S 672 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER S 677 " --> pdb=" O PRO S 673 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN S 681 " --> pdb=" O SER S 677 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN S 684 " --> pdb=" O ASP S 680 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR S 685 " --> pdb=" O GLN S 681 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR S 686 " --> pdb=" O PHE S 682 " (cutoff:3.500A) Processing helix chain 'S' and resid 710 through 715 Processing helix chain 'S' and resid 730 through 742 removed outlier: 4.191A pdb=" N GLU S 735 " --> pdb=" O LEU S 731 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE S 736 " --> pdb=" O LEU S 732 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL S 737 " --> pdb=" O THR S 733 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS S 738 " --> pdb=" O LYS S 734 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP S 739 " --> pdb=" O GLU S 735 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 3.919A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG S 762 " --> pdb=" O ASN S 758 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 32 removed outlier: 3.504A pdb=" N ARG R 16 " --> pdb=" O LYS R 12 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR R 26 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG R 29 " --> pdb=" O ASN R 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG R 30 " --> pdb=" O TYR R 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 158 through 163 removed outlier: 3.678A pdb=" N LYS R 163 " --> pdb=" O TYR R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 173 removed outlier: 3.532A pdb=" N ARG R 171 " --> pdb=" O LYS R 167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 removed outlier: 3.966A pdb=" N LEU R 178 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 removed outlier: 3.833A pdb=" N LYS R 185 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE R 188 " --> pdb=" O ASN R 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE R 191 " --> pdb=" O TYR R 187 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 204 removed outlier: 3.871A pdb=" N SER R 203 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU R 204 " --> pdb=" O SER R 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 200 through 204' Processing helix chain 'R' and resid 210 through 225 removed outlier: 3.958A pdb=" N VAL R 214 " --> pdb=" O THR R 210 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN R 223 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 4.147A pdb=" N ALA R 232 " --> pdb=" O ASN R 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR R 233 " --> pdb=" O TRP R 229 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 236 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA R 237 " --> pdb=" O TYR R 233 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 252 removed outlier: 4.362A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 247 through 252' Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.765A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 275 removed outlier: 4.092A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP R 273 " --> pdb=" O ASP R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 4.355A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 322 removed outlier: 3.630A pdb=" N LEU R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE R 318 " --> pdb=" O TRP R 314 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 350 Processing helix chain 'R' and resid 350 through 355 removed outlier: 3.511A pdb=" N LEU R 354 " --> pdb=" O SER R 350 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR R 355 " --> pdb=" O GLU R 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 350 through 355' Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.659A pdb=" N PHE R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 379 removed outlier: 4.097A pdb=" N THR R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 374 through 379' Processing helix chain 'R' and resid 400 through 405 Processing helix chain 'R' and resid 405 through 413 removed outlier: 4.219A pdb=" N HIS R 409 " --> pdb=" O ILE R 405 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL R 411 " --> pdb=" O HIS R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 421 Processing helix chain 'R' and resid 429 through 439 removed outlier: 3.594A pdb=" N ASN R 433 " --> pdb=" O ARG R 429 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU R 439 " --> pdb=" O LEU R 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.044A pdb=" N LEU A 27 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.172A pdb=" N ASN A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.726A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.554A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.589A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 4.259A pdb=" N LEU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.520A pdb=" N ILE A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.629A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.931A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.845A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.551A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.835A pdb=" N ALA A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.772A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.738A pdb=" N GLY A 622 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.750A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.905A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.160A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 793 through 801 removed outlier: 3.819A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.705A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 4.067A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 849 removed outlier: 3.955A pdb=" N LYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 removed outlier: 3.854A pdb=" N GLU A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.765A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 923 through 930 removed outlier: 3.625A pdb=" N MET A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.729A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1004 Processing helix chain 'A' and resid 1005 through 1012 removed outlier: 3.695A pdb=" N ALA A1010 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A1012 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 3.919A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 3.670A pdb=" N GLY A1052 " --> pdb=" O MET A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1063 removed outlier: 4.561A pdb=" N HIS A1062 " --> pdb=" O LYS A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 removed outlier: 3.521A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1104 removed outlier: 4.276A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.765A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.923A pdb=" N ASP A1142 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A1143 " --> pdb=" O ASN A1139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.978A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A1174 " --> pdb=" O MET A1170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1190 removed outlier: 3.562A pdb=" N SER A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.962A pdb=" N THR A1198 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 removed outlier: 4.160A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1259 removed outlier: 4.233A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1258 " --> pdb=" O PHE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.553A pdb=" N TYR A1302 " --> pdb=" O ASP A1298 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 Processing helix chain 'A' and resid 1320 through 1339 removed outlier: 3.799A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR A1339 " --> pdb=" O LYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1379 removed outlier: 3.675A pdb=" N HIS A1375 " --> pdb=" O GLU A1371 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A1377 " --> pdb=" O GLN A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1393 removed outlier: 3.852A pdb=" N ILE A1392 " --> pdb=" O GLU A1389 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A1393 " --> pdb=" O ASP A1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1389 through 1393' Processing helix chain 'A' and resid 1440 through 1452 removed outlier: 3.690A pdb=" N ASP A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 removed outlier: 3.634A pdb=" N VAL A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.698A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 3.934A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1571 removed outlier: 3.871A pdb=" N ILE A1562 " --> pdb=" O ALA A1558 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.689A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.822A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1627 removed outlier: 3.697A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1625 " --> pdb=" O PHE A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 Processing helix chain 'B' and resid 21 through 26 removed outlier: 4.093A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.080A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.779A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 4.134A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.974A pdb=" N SER B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 89' Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.658A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 226 removed outlier: 4.639A pdb=" N ASN B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.481A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.870A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.640A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.813A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.693A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.911A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 430 Processing helix chain 'B' and resid 442 through 451 removed outlier: 4.012A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.644A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.940A pdb=" N VAL B 517 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.594A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.877A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.761A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.812A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 711 through 714 Processing helix chain 'B' and resid 715 through 724 removed outlier: 3.539A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.979A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 760 removed outlier: 4.395A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 760 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 760' Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 835 through 839 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.821A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 969 removed outlier: 3.887A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 973 Processing helix chain 'B' and resid 991 through 996 Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.873A pdb=" N ALA B1001 " --> pdb=" O GLY B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1080 removed outlier: 3.697A pdb=" N ARG B1076 " --> pdb=" O GLY B1072 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1093 Processing helix chain 'B' and resid 1179 through 1191 removed outlier: 4.028A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.674A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.646A pdb=" N LEU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.127A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.594A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.697A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.711A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 33 through 44 removed outlier: 3.514A pdb=" N LEU D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.834A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 removed outlier: 4.475A pdb=" N PHE D 96 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 27 removed outlier: 4.328A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.554A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.557A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.552A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 166 removed outlier: 4.414A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.984A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.970A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.824A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.725A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 4.032A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 149 through 152 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'J' and resid 31 through 36 removed outlier: 3.594A pdb=" N ALA J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 removed outlier: 3.761A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.997A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.695A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN K 74 " --> pdb=" O HIS K 70 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.899A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU K 132 " --> pdb=" O CYS K 128 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 removed outlier: 3.860A pdb=" N LYS N 66 " --> pdb=" O ASP N 63 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU N 67 " --> pdb=" O ILE N 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 63 through 67' Processing helix chain 'O' and resid 49 through 61 removed outlier: 3.713A pdb=" N SER O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL O 56 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.930A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.834A pdb=" N ASP O 98 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.557A pdb=" N GLU O 127 " --> pdb=" O LYS O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 4.009A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE O 147 " --> pdb=" O LEU O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.950A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU O 158 " --> pdb=" O VAL O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 164 No H-bonds generated for 'chain 'O' and resid 162 through 164' Processing helix chain 'O' and resid 171 through 183 removed outlier: 3.812A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 3.773A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 210 removed outlier: 3.625A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 222 removed outlier: 4.761A pdb=" N LEU O 218 " --> pdb=" O ASN O 214 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG O 219 " --> pdb=" O LEU O 215 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 242 removed outlier: 3.611A pdb=" N TRP O 230 " --> pdb=" O GLY O 226 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 345 removed outlier: 4.162A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR O 337 " --> pdb=" O ASP O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 353 removed outlier: 3.934A pdb=" N GLU O 353 " --> pdb=" O PRO O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 372 removed outlier: 3.834A pdb=" N THR O 363 " --> pdb=" O GLY O 359 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR O 366 " --> pdb=" O ASN O 362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR O 370 " --> pdb=" O THR O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 389 removed outlier: 4.311A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 408 removed outlier: 3.852A pdb=" N ASP O 405 " --> pdb=" O VAL O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 429 removed outlier: 3.684A pdb=" N LYS O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR O 427 " --> pdb=" O TYR O 423 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 437 through 453 removed outlier: 3.589A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA O 443 " --> pdb=" O ILE O 439 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.565A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 487 removed outlier: 3.511A pdb=" N ALA O 476 " --> pdb=" O HIS O 472 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 483 " --> pdb=" O ALA O 479 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE O 484 " --> pdb=" O LEU O 480 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE O 486 " --> pdb=" O TYR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 511 removed outlier: 4.706A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE O 511 " --> pdb=" O GLN O 507 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.600A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS O 520 " --> pdb=" O PRO O 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 515 through 520' Processing helix chain 'O' and resid 521 through 533 Processing helix chain 'O' and resid 540 through 546 Processing helix chain 'O' and resid 582 through 590 removed outlier: 3.596A pdb=" N ASP O 587 " --> pdb=" O GLN O 583 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU O 588 " --> pdb=" O GLN O 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN O 589 " --> pdb=" O PHE O 585 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 14.41 Time building geometry restraints manager: 13.73 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: 14175 1.33 - 1.45: 10841 1.45 - 1.58: 26502 1.58 - 1.70: 154 1.70 - 1.82: 370 Bond restraints: 52042 Sorted by residual: bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.331 1.373 -0.041 7.90e-03 1.60e+04 2.74e+01 bond pdb=" C ILE B 943 " pdb=" N GLN B 944 " ideal model delta sigma weight residual 1.335 1.210 0.125 3.04e-02 1.08e+03 1.69e+01 bond pdb=" N ILE B 977 " pdb=" CA ILE B 977 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.15e-02 7.56e+03 1.20e+01 bond pdb=" N ILE B1026 " pdb=" CA ILE B1026 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.67e+00 bond pdb=" N GLU Q 246 " pdb=" CA GLU Q 246 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.48e+00 ... (remaining 52037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 67440 2.29 - 4.58: 2805 4.58 - 6.88: 308 6.88 - 9.17: 85 9.17 - 11.46: 18 Bond angle restraints: 70656 Sorted by residual: angle pdb=" N ILE O 107 " pdb=" CA ILE O 107 " pdb=" C ILE O 107 " ideal model delta sigma weight residual 113.71 105.62 8.09 9.50e-01 1.11e+00 7.25e+01 angle pdb=" C ARG B 560 " pdb=" N ILE B 561 " pdb=" CA ILE B 561 " ideal model delta sigma weight residual 120.24 124.64 -4.40 6.30e-01 2.52e+00 4.88e+01 angle pdb=" C SER J 20 " pdb=" N TYR J 21 " pdb=" CA TYR J 21 " ideal model delta sigma weight residual 122.11 111.13 10.98 1.64e+00 3.72e-01 4.48e+01 angle pdb=" N ILE B 457 " pdb=" CA ILE B 457 " pdb=" C ILE B 457 " ideal model delta sigma weight residual 112.29 106.12 6.17 9.40e-01 1.13e+00 4.31e+01 angle pdb=" C GLU I 18 " pdb=" N ASN I 19 " pdb=" CA ASN I 19 " ideal model delta sigma weight residual 120.83 130.00 -9.17 1.43e+00 4.89e-01 4.11e+01 ... (remaining 70651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 30853 35.15 - 70.29: 536 70.29 - 105.44: 28 105.44 - 140.59: 4 140.59 - 175.73: 5 Dihedral angle restraints: 31426 sinusoidal: 13429 harmonic: 17997 Sorted by residual: dihedral pdb=" CA PRO B1118 " pdb=" C PRO B1118 " pdb=" N ARG B1119 " pdb=" CA ARG B1119 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE Q 23 " pdb=" C ILE Q 23 " pdb=" N ASP Q 24 " pdb=" CA ASP Q 24 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR J 44 " pdb=" C TYR J 44 " pdb=" N CYS J 45 " pdb=" CA CYS J 45 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 31423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 7014 0.093 - 0.185: 824 0.185 - 0.278: 45 0.278 - 0.371: 3 0.371 - 0.463: 1 Chirality restraints: 7887 Sorted by residual: chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CB VAL A1011 " pdb=" CA VAL A1011 " pdb=" CG1 VAL A1011 " pdb=" CG2 VAL A1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL A 587 " pdb=" CA VAL A 587 " pdb=" CG1 VAL A 587 " pdb=" CG2 VAL A 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 7884 not shown) Planarity restraints: 8789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B1023 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ARG B1023 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG B1023 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B1024 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 668 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY A 668 " 0.056 2.00e-02 2.50e+03 pdb=" O GLY A 668 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 669 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 712 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO B 713 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 713 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 713 " 0.044 5.00e-02 4.00e+02 ... (remaining 8786 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 657 2.61 - 3.18: 42089 3.18 - 3.75: 77265 3.75 - 4.33: 107474 4.33 - 4.90: 170062 Nonbonded interactions: 397547 Sorted by model distance: nonbonded pdb=" O GLY A 668 " pdb=" O LEU A 669 " model vdw 2.036 3.040 nonbonded pdb=" O GLN M 75 " pdb=" O TYR M 76 " model vdw 2.147 3.040 nonbonded pdb=" O CYS R 275 " pdb=" OG SER R 279 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN A 840 " pdb=" OG1 THR A 844 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 951 " pdb=" OG1 THR I 98 " model vdw 2.237 3.040 ... (remaining 397542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.900 Check model and map are aligned: 0.350 Set scattering table: 0.480 Process input model: 104.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.210 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 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 0.125 52042 Z= 0.503 Angle : 1.071 11.458 70656 Z= 0.595 Chirality : 0.060 0.463 7887 Planarity : 0.007 0.078 8789 Dihedral : 13.216 175.732 19743 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.53 % Favored : 89.32 % Rotamer: Outliers : 0.58 % Allowed : 3.37 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.08), residues: 6049 helix: -4.19 (0.06), residues: 1916 sheet: -3.22 (0.17), residues: 680 loop : -3.15 (0.09), residues: 3453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 984 HIS 0.026 0.003 HIS B 532 PHE 0.032 0.004 PHE O 585 TYR 0.047 0.003 TYR B1098 ARG 0.017 0.001 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1374 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 21 ARG cc_start: 0.1023 (pmt-80) cc_final: 0.0633 (tpp80) REVERT: Q 114 ARG cc_start: 0.3547 (mmm-85) cc_final: 0.3125 (mmm160) REVERT: Q 215 LEU cc_start: 0.2663 (tp) cc_final: 0.1895 (tp) REVERT: Q 238 HIS cc_start: 0.4963 (m90) cc_final: 0.4700 (m-70) REVERT: Q 255 LYS cc_start: 0.1942 (tttt) cc_final: 0.1690 (ttmt) REVERT: Q 287 TRP cc_start: 0.1842 (t60) cc_final: 0.0908 (t60) REVERT: Q 292 GLU cc_start: 0.1743 (pm20) cc_final: 0.1215 (mp0) REVERT: Q 301 HIS cc_start: 0.4153 (m90) cc_final: 0.3232 (t70) REVERT: S 35 LYS cc_start: 0.3096 (pttt) cc_final: 0.2601 (tttt) REVERT: S 47 ASP cc_start: 0.3530 (p0) cc_final: 0.2506 (p0) REVERT: S 221 ARG cc_start: 0.4807 (ttt90) cc_final: 0.3077 (ptt180) REVERT: S 235 SER cc_start: 0.5210 (p) cc_final: 0.4937 (p) REVERT: S 369 PHE cc_start: 0.3943 (t80) cc_final: 0.2543 (m-10) REVERT: S 380 MET cc_start: 0.1599 (ttp) cc_final: 0.0783 (ttp) REVERT: S 386 MET cc_start: 0.3503 (tpp) cc_final: 0.3146 (tpp) REVERT: S 399 TRP cc_start: 0.1010 (m-90) cc_final: -0.2194 (m100) REVERT: S 433 VAL cc_start: 0.5507 (m) cc_final: 0.4905 (m) REVERT: S 667 ASP cc_start: -0.0566 (t0) cc_final: -0.1249 (t0) REVERT: S 675 PHE cc_start: 0.2908 (t80) cc_final: 0.1578 (t80) REVERT: S 689 GLN cc_start: 0.4621 (mm-40) cc_final: 0.2967 (pp30) REVERT: S 691 VAL cc_start: 0.3062 (p) cc_final: 0.2256 (t) REVERT: S 693 PHE cc_start: 0.1263 (m-80) cc_final: -0.0526 (p90) REVERT: S 777 MET cc_start: 0.2487 (ttp) cc_final: 0.2080 (tpt) REVERT: R 23 TYR cc_start: 0.0874 (t80) cc_final: 0.0361 (t80) REVERT: R 290 TYR cc_start: 0.4243 (m-80) cc_final: 0.3841 (m-80) REVERT: R 291 ARG cc_start: 0.4463 (mpt180) cc_final: 0.2160 (tpt-90) REVERT: R 307 LYS cc_start: 0.3296 (mmmt) cc_final: 0.2765 (tttm) REVERT: A 22 LYS cc_start: 0.6969 (mmmm) cc_final: 0.6020 (mttt) REVERT: A 130 ILE cc_start: 0.8122 (mt) cc_final: 0.7875 (mt) REVERT: A 314 TYR cc_start: 0.6629 (t80) cc_final: 0.6407 (t80) REVERT: A 347 ARG cc_start: 0.6561 (ptp90) cc_final: 0.5773 (ttt90) REVERT: A 491 GLU cc_start: 0.7009 (mm-30) cc_final: 0.5978 (mm-30) REVERT: A 509 GLU cc_start: 0.7556 (tp30) cc_final: 0.7330 (tp30) REVERT: A 545 SER cc_start: 0.8430 (t) cc_final: 0.8165 (m) REVERT: A 557 LEU cc_start: 0.8038 (tt) cc_final: 0.7807 (tp) REVERT: A 653 THR cc_start: 0.8487 (p) cc_final: 0.8136 (t) REVERT: A 819 ASN cc_start: 0.7342 (m110) cc_final: 0.7127 (t0) REVERT: A 827 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8238 (p) REVERT: A 953 GLU cc_start: 0.7757 (pt0) cc_final: 0.7015 (mm-30) REVERT: A 960 MET cc_start: 0.7971 (mtt) cc_final: 0.7725 (mtp) REVERT: A 1092 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7098 (tm-30) REVERT: A 1245 ASP cc_start: 0.6284 (p0) cc_final: 0.5772 (m-30) REVERT: A 1246 VAL cc_start: 0.8431 (p) cc_final: 0.7407 (t) REVERT: A 1265 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6503 (mt-10) REVERT: A 1306 TYR cc_start: 0.5551 (m-80) cc_final: 0.5026 (m-80) REVERT: A 1535 PHE cc_start: 0.6862 (m-80) cc_final: 0.6411 (m-80) REVERT: A 1600 ARG cc_start: 0.7591 (mtm180) cc_final: 0.6402 (mtp85) REVERT: B 66 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7725 (mtpp) REVERT: B 316 ARG cc_start: 0.7255 (tpt90) cc_final: 0.7055 (tpt-90) REVERT: B 371 PHE cc_start: 0.8854 (t80) cc_final: 0.8625 (t80) REVERT: B 383 SER cc_start: 0.8519 (t) cc_final: 0.8300 (t) REVERT: B 429 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6580 (mtp180) REVERT: B 441 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7402 (mttm) REVERT: B 444 ARG cc_start: 0.8372 (ptp90) cc_final: 0.7977 (ptp90) REVERT: B 461 MET cc_start: 0.7172 (mmm) cc_final: 0.6521 (mmt) REVERT: B 480 GLN cc_start: 0.5371 (pm20) cc_final: 0.5031 (pm20) REVERT: B 489 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6841 (mt-10) REVERT: B 495 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7722 (tpt170) REVERT: B 519 LYS cc_start: 0.7389 (ttmp) cc_final: 0.6872 (mmpt) REVERT: B 550 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7030 (ptt90) REVERT: B 554 GLN cc_start: 0.7819 (pm20) cc_final: 0.7314 (mt0) REVERT: B 576 THR cc_start: 0.8010 (m) cc_final: 0.7771 (t) REVERT: B 591 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8263 (tttp) REVERT: B 740 LYS cc_start: 0.8314 (ptpp) cc_final: 0.8036 (pttm) REVERT: B 752 VAL cc_start: 0.9014 (t) cc_final: 0.8758 (p) REVERT: B 943 ILE cc_start: 0.8312 (mt) cc_final: 0.8075 (mt) REVERT: B 1049 THR cc_start: 0.8349 (t) cc_final: 0.8116 (m) REVERT: B 1057 MET cc_start: 0.8155 (mmm) cc_final: 0.7755 (ttm) REVERT: B 1188 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6943 (mm-30) REVERT: C 74 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 227 TYR cc_start: 0.9167 (p90) cc_final: 0.8945 (p90) REVERT: C 278 GLU cc_start: 0.6766 (tp30) cc_final: 0.6518 (tp30) REVERT: C 327 TYR cc_start: 0.7974 (t80) cc_final: 0.7424 (t80) REVERT: E 98 ILE cc_start: 0.7691 (mt) cc_final: 0.7385 (mm) REVERT: F 144 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7295 (mt-10) REVERT: G 58 LEU cc_start: 0.5999 (mt) cc_final: 0.5511 (mp) REVERT: G 88 LYS cc_start: 0.8282 (ttpp) cc_final: 0.8043 (mttt) REVERT: G 126 GLN cc_start: 0.7614 (tt0) cc_final: 0.6768 (tt0) REVERT: G 168 PHE cc_start: 0.3716 (t80) cc_final: 0.3463 (t80) REVERT: H 8 ASP cc_start: 0.7617 (t0) cc_final: 0.7221 (t70) REVERT: H 111 LEU cc_start: 0.5924 (mt) cc_final: 0.5579 (mp) REVERT: H 145 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.7059 (ttp80) REVERT: I 60 LEU cc_start: 0.8497 (tt) cc_final: 0.7985 (mp) REVERT: J 68 LYS cc_start: 0.6914 (tttp) cc_final: 0.5837 (mmtp) REVERT: K 44 ARG cc_start: 0.6782 (ptp-170) cc_final: 0.6491 (ptp-170) REVERT: K 60 SER cc_start: 0.8021 (m) cc_final: 0.7802 (t) REVERT: K 69 ASP cc_start: 0.7681 (p0) cc_final: 0.7388 (t0) REVERT: K 107 THR cc_start: 0.8200 (p) cc_final: 0.7998 (p) REVERT: L 42 ARG cc_start: 0.6221 (ptt-90) cc_final: 0.5538 (mmt-90) REVERT: N 80 MET cc_start: 0.3958 (ttp) cc_final: 0.3071 (tmm) REVERT: N 154 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.1921 (ttp80) REVERT: O 178 TYR cc_start: 0.5711 (t80) cc_final: 0.4218 (m-10) REVERT: O 369 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7557 (pptt) REVERT: O 382 GLN cc_start: 0.6769 (pm20) cc_final: 0.6177 (mt0) REVERT: O 467 MET cc_start: 0.6677 (mmp) cc_final: 0.6378 (mmt) REVERT: O 498 TRP cc_start: 0.4672 (m100) cc_final: 0.4393 (m-90) REVERT: O 541 PHE cc_start: 0.5596 (t80) cc_final: 0.5377 (t80) REVERT: O 583 GLN cc_start: 0.6931 (tp40) cc_final: 0.6522 (pm20) outliers start: 32 outliers final: 5 residues processed: 1403 average time/residue: 0.6839 time to fit residues: 1535.9171 Evaluate side-chains 769 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 762 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 975 HIS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 518 optimal weight: 1.9990 chunk 465 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 313 optimal weight: 0.0970 chunk 248 optimal weight: 0.6980 chunk 481 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 557 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 14 ASN Q 33 HIS Q 42 ASN Q 351 ASN Q 511 HIS S 180 ASN ** S 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 483 HIS S 487 ASN S 554 ASN S 613 HIS S 665 ASN S 758 ASN R 25 ASN R 179 HIS R 207 ASN R 287 ASN R 433 ASN R 434 GLN M 71 GLN M 89 GLN A 60 ASN A 264 ASN A 332 GLN A 431 GLN A 470 HIS A 537 GLN A 560 GLN A 592 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 748 ASN A 753 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A 937 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1314 GLN A1447 GLN B 62 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 328 GLN B 433 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 598 HIS B 673 ASN B 686 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN B 923 GLN B1066 HIS ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 216 HIS ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS E 61 GLN G 26 ASN G 67 ASN ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 150 HIS I 91 ASN I 95 ASN J 53 HIS K 106 GLN L 53 HIS O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52042 Z= 0.204 Angle : 0.688 10.325 70656 Z= 0.367 Chirality : 0.046 0.279 7887 Planarity : 0.006 0.084 8789 Dihedral : 13.924 173.816 7528 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.98 % Favored : 92.00 % Rotamer: Outliers : 2.59 % Allowed : 10.96 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.09), residues: 6049 helix: -3.11 (0.08), residues: 2011 sheet: -2.95 (0.18), residues: 658 loop : -2.72 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 722 HIS 0.009 0.001 HIS B 532 PHE 0.029 0.002 PHE E 135 TYR 0.026 0.002 TYR R 410 ARG 0.008 0.001 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 882 time to evaluate : 5.945 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: Q 21 ARG cc_start: 0.1183 (pmt-80) cc_final: 0.0460 (tpp80) REVERT: Q 287 TRP cc_start: 0.1392 (t60) cc_final: 0.0881 (t60) REVERT: Q 292 GLU cc_start: 0.1683 (pm20) cc_final: 0.1244 (mp0) REVERT: Q 301 HIS cc_start: 0.4187 (m90) cc_final: 0.3177 (t-90) REVERT: S 33 THR cc_start: 0.2114 (t) cc_final: 0.1887 (m) REVERT: S 221 ARG cc_start: 0.4747 (ttt90) cc_final: 0.3664 (ttp80) REVERT: S 256 ARG cc_start: 0.2311 (ptm-80) cc_final: 0.1845 (ptp-170) REVERT: S 369 PHE cc_start: 0.3860 (t80) cc_final: 0.2641 (m-10) REVERT: S 386 MET cc_start: 0.3648 (tpp) cc_final: 0.3299 (tpp) REVERT: S 470 SER cc_start: 0.3367 (t) cc_final: 0.3112 (t) REVERT: S 471 MET cc_start: 0.0695 (tmm) cc_final: -0.0201 (tmm) REVERT: S 484 ARG cc_start: 0.6801 (mmm-85) cc_final: 0.5801 (mtt180) REVERT: S 667 ASP cc_start: -0.1109 (t0) cc_final: -0.1383 (t0) REVERT: S 691 VAL cc_start: 0.3245 (p) cc_final: 0.2778 (t) REVERT: S 693 PHE cc_start: 0.0956 (m-80) cc_final: -0.0642 (p90) REVERT: S 772 ILE cc_start: 0.4130 (mm) cc_final: 0.3799 (pt) REVERT: R 23 TYR cc_start: 0.0927 (t80) cc_final: 0.0677 (t80) REVERT: R 287 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6306 (t0) REVERT: R 291 ARG cc_start: 0.4202 (mpt180) cc_final: 0.2017 (tpt-90) REVERT: R 307 LYS cc_start: 0.3093 (mmmt) cc_final: 0.2577 (tttm) REVERT: M 42 LYS cc_start: 0.5024 (pptt) cc_final: 0.4614 (ttmt) REVERT: A 22 LYS cc_start: 0.7107 (mmmm) cc_final: 0.5943 (mttt) REVERT: A 129 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6653 (pp) REVERT: A 130 ILE cc_start: 0.8264 (mt) cc_final: 0.8027 (mt) REVERT: A 336 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7614 (tp40) REVERT: A 347 ARG cc_start: 0.6936 (ptp90) cc_final: 0.5922 (ttt90) REVERT: A 420 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6713 (t80) REVERT: A 491 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6121 (mm-30) REVERT: A 509 GLU cc_start: 0.7591 (tp30) cc_final: 0.7285 (tp30) REVERT: A 601 MET cc_start: 0.8422 (mtm) cc_final: 0.8200 (mtm) REVERT: A 633 MET cc_start: 0.8052 (mtt) cc_final: 0.7832 (ttm) REVERT: A 653 THR cc_start: 0.8472 (p) cc_final: 0.8210 (t) REVERT: A 693 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: A 785 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8016 (mm110) REVERT: A 953 GLU cc_start: 0.7772 (pt0) cc_final: 0.7012 (mm-30) REVERT: A 960 MET cc_start: 0.7923 (mtt) cc_final: 0.7700 (mtp) REVERT: A 1000 MET cc_start: 0.8485 (mtp) cc_final: 0.8222 (mtp) REVERT: A 1018 TYR cc_start: 0.8054 (t80) cc_final: 0.7737 (t80) REVERT: A 1020 GLN cc_start: 0.7810 (tt0) cc_final: 0.7606 (tt0) REVERT: A 1092 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7026 (tm-30) REVERT: A 1139 ASN cc_start: 0.8221 (t0) cc_final: 0.8015 (t0) REVERT: A 1245 ASP cc_start: 0.6189 (p0) cc_final: 0.5857 (m-30) REVERT: A 1246 VAL cc_start: 0.7920 (p) cc_final: 0.7679 (t) REVERT: A 1265 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 1444 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7199 (mtt90) REVERT: A 1533 GLU cc_start: 0.6653 (pm20) cc_final: 0.6386 (tp30) REVERT: A 1535 PHE cc_start: 0.6654 (m-80) cc_final: 0.6332 (m-80) REVERT: A 1600 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6686 (mtp180) REVERT: B 43 GLN cc_start: 0.7922 (tp40) cc_final: 0.7235 (tt0) REVERT: B 229 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6212 (t80) REVERT: B 237 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8452 (ttt-90) REVERT: B 261 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: B 335 ARG cc_start: 0.7116 (ttt90) cc_final: 0.6626 (ttp-110) REVERT: B 441 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7327 (mttp) REVERT: B 444 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7828 (tpt170) REVERT: B 461 MET cc_start: 0.7267 (mmm) cc_final: 0.6143 (mmt) REVERT: B 495 ARG cc_start: 0.7927 (tpt90) cc_final: 0.7581 (tpt170) REVERT: B 550 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7060 (ptt90) REVERT: B 554 GLN cc_start: 0.7533 (pm20) cc_final: 0.7269 (mt0) REVERT: B 588 ILE cc_start: 0.8525 (pt) cc_final: 0.8323 (pt) REVERT: B 591 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8254 (tttp) REVERT: B 740 LYS cc_start: 0.8278 (ptpp) cc_final: 0.8051 (mttt) REVERT: B 943 ILE cc_start: 0.8348 (mt) cc_final: 0.7735 (mm) REVERT: B 970 LYS cc_start: 0.6393 (ttpt) cc_final: 0.6046 (ptmt) REVERT: B 1013 MET cc_start: 0.4706 (tmm) cc_final: 0.4051 (tmm) REVERT: B 1049 THR cc_start: 0.8225 (t) cc_final: 0.7996 (m) REVERT: B 1057 MET cc_start: 0.8290 (mmm) cc_final: 0.7938 (ttm) REVERT: B 1134 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6376 (mtt180) REVERT: B 1151 ILE cc_start: 0.4833 (OUTLIER) cc_final: 0.4309 (pp) REVERT: B 1157 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6446 (mm-40) REVERT: B 1188 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 57 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8117 (mt) REVERT: C 124 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: C 278 GLU cc_start: 0.6739 (tp30) cc_final: 0.6492 (tp30) REVERT: C 319 ARG cc_start: 0.6796 (mtm180) cc_final: 0.6596 (mtt90) REVERT: C 327 TYR cc_start: 0.7996 (t80) cc_final: 0.7748 (t80) REVERT: F 144 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7572 (mt-10) REVERT: G 21 LYS cc_start: 0.7398 (mttt) cc_final: 0.6721 (tmtt) REVERT: G 88 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7968 (mttt) REVERT: G 126 GLN cc_start: 0.7248 (tt0) cc_final: 0.7042 (tt0) REVERT: H 49 VAL cc_start: 0.8481 (t) cc_final: 0.8278 (m) REVERT: H 145 ARG cc_start: 0.7076 (ttp-110) cc_final: 0.6544 (ttm-80) REVERT: J 68 LYS cc_start: 0.6752 (tttp) cc_final: 0.5812 (mmtp) REVERT: L 42 ARG cc_start: 0.6144 (ptt-90) cc_final: 0.5627 (mmt-90) REVERT: N 36 LYS cc_start: 0.2738 (mmtt) cc_final: 0.1497 (ptpp) REVERT: N 80 MET cc_start: 0.3796 (ttp) cc_final: 0.3254 (tmm) REVERT: O 137 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7236 (mp) REVERT: O 151 TRP cc_start: 0.6704 (t-100) cc_final: 0.6393 (t-100) REVERT: O 369 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7575 (tmmt) REVERT: O 382 GLN cc_start: 0.6941 (pm20) cc_final: 0.6396 (mt0) REVERT: O 486 PHE cc_start: 0.4897 (m-10) cc_final: 0.4292 (m-10) REVERT: O 541 PHE cc_start: 0.5562 (t80) cc_final: 0.5356 (t80) REVERT: O 583 GLN cc_start: 0.6858 (tp40) cc_final: 0.6644 (pm20) outliers start: 142 outliers final: 73 residues processed: 979 average time/residue: 0.7125 time to fit residues: 1147.9683 Evaluate side-chains 758 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 675 time to evaluate : 5.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 555 THR Chi-restraints excluded: chain S residue 637 LEU Chi-restraints excluded: chain S residue 736 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 286 GLN Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 167 LYS Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 309 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 464 optimal weight: 0.6980 chunk 379 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 558 optimal weight: 5.9990 chunk 603 optimal weight: 4.9990 chunk 497 optimal weight: 0.0040 chunk 553 optimal weight: 0.5980 chunk 190 optimal weight: 9.9990 chunk 448 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 479 HIS S 758 ASN R 150 GLN A 107 HIS ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1062 HIS A1319 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 683 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 234 ASN ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 153 HIS ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN K 64 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 438 GLN O 547 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52042 Z= 0.172 Angle : 0.607 10.580 70656 Z= 0.321 Chirality : 0.044 0.221 7887 Planarity : 0.005 0.074 8789 Dihedral : 13.586 175.041 7523 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.24 % Favored : 92.74 % Rotamer: Outliers : 2.75 % Allowed : 12.29 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.09), residues: 6049 helix: -2.48 (0.09), residues: 2034 sheet: -2.69 (0.18), residues: 658 loop : -2.49 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 722 HIS 0.008 0.001 HIS A1454 PHE 0.020 0.001 PHE E 60 TYR 0.024 0.001 TYR O 602 ARG 0.009 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 778 time to evaluate : 5.799 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: Q 21 ARG cc_start: 0.0565 (pmt-80) cc_final: 0.0161 (tpp80) REVERT: Q 164 ILE cc_start: 0.1985 (OUTLIER) cc_final: 0.1693 (tt) REVERT: Q 287 TRP cc_start: 0.1259 (t60) cc_final: 0.0721 (t60) REVERT: Q 292 GLU cc_start: 0.2114 (pm20) cc_final: 0.1632 (mp0) REVERT: Q 301 HIS cc_start: 0.4311 (m90) cc_final: 0.3264 (t-90) REVERT: S 221 ARG cc_start: 0.5103 (ttt90) cc_final: 0.3512 (ptt180) REVERT: S 362 ARG cc_start: 0.1131 (tpt90) cc_final: 0.0860 (mmm-85) REVERT: S 386 MET cc_start: 0.3761 (tpp) cc_final: 0.3381 (tpp) REVERT: S 399 TRP cc_start: 0.1289 (m-90) cc_final: -0.2240 (m100) REVERT: S 471 MET cc_start: 0.0605 (tmm) cc_final: -0.0395 (tmm) REVERT: S 484 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.5839 (mtt180) REVERT: S 667 ASP cc_start: -0.1189 (t0) cc_final: -0.1470 (t0) REVERT: S 693 PHE cc_start: 0.0761 (m-80) cc_final: -0.0689 (p90) REVERT: S 772 ILE cc_start: 0.4035 (mm) cc_final: 0.3746 (pt) REVERT: S 777 MET cc_start: 0.1806 (ttp) cc_final: 0.0871 (tpt) REVERT: R 23 TYR cc_start: 0.0968 (t80) cc_final: 0.0690 (t80) REVERT: R 236 PHE cc_start: 0.3784 (t80) cc_final: 0.3510 (t80) REVERT: R 283 ARG cc_start: 0.4565 (ttp-170) cc_final: 0.4303 (ttp80) REVERT: R 291 ARG cc_start: 0.4127 (mpt180) cc_final: 0.2049 (tpt-90) REVERT: R 302 ARG cc_start: 0.3925 (mtt-85) cc_final: 0.3576 (ptp-170) REVERT: R 307 LYS cc_start: 0.3278 (mmmt) cc_final: 0.2739 (tttm) REVERT: M 42 LYS cc_start: 0.5229 (pptt) cc_final: 0.4575 (mttp) REVERT: A 22 LYS cc_start: 0.7089 (mmmm) cc_final: 0.5967 (mttt) REVERT: A 347 ARG cc_start: 0.6975 (ptp90) cc_final: 0.5956 (ttt90) REVERT: A 420 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6715 (t80) REVERT: A 424 MET cc_start: 0.6910 (mmp) cc_final: 0.5837 (ptm) REVERT: A 491 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 509 GLU cc_start: 0.7576 (tp30) cc_final: 0.7202 (tp30) REVERT: A 601 MET cc_start: 0.8368 (mtm) cc_final: 0.8140 (ptp) REVERT: A 633 MET cc_start: 0.7963 (mtt) cc_final: 0.7754 (ttm) REVERT: A 785 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8036 (mm110) REVERT: A 928 MET cc_start: 0.8437 (ptp) cc_final: 0.8122 (ptp) REVERT: A 953 GLU cc_start: 0.7796 (pt0) cc_final: 0.7130 (mm-30) REVERT: A 960 MET cc_start: 0.7887 (mtt) cc_final: 0.7655 (mtp) REVERT: A 1092 GLU cc_start: 0.7782 (mm-30) cc_final: 0.6947 (tm-30) REVERT: A 1444 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7233 (mmt90) REVERT: A 1533 GLU cc_start: 0.6476 (pm20) cc_final: 0.6201 (tp30) REVERT: A 1535 PHE cc_start: 0.6573 (m-80) cc_final: 0.6276 (m-80) REVERT: A 1600 ARG cc_start: 0.7611 (mtm180) cc_final: 0.6556 (mtp-110) REVERT: B 43 GLN cc_start: 0.7861 (tp40) cc_final: 0.7251 (tt0) REVERT: B 229 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.5820 (t80) REVERT: B 237 ARG cc_start: 0.8745 (ttt-90) cc_final: 0.8405 (ttt-90) REVERT: B 261 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.8087 (ttt180) REVERT: B 268 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6278 (mm-30) REVERT: B 335 ARG cc_start: 0.7100 (ttt90) cc_final: 0.6594 (ttp-110) REVERT: B 441 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7293 (mttp) REVERT: B 444 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7794 (tpt170) REVERT: B 461 MET cc_start: 0.7396 (mmm) cc_final: 0.6079 (mmt) REVERT: B 495 ARG cc_start: 0.7891 (tpt90) cc_final: 0.7631 (tpt170) REVERT: B 519 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6956 (mmtm) REVERT: B 550 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.7019 (ptt90) REVERT: B 575 HIS cc_start: 0.7004 (m90) cc_final: 0.6789 (m170) REVERT: B 588 ILE cc_start: 0.8542 (pt) cc_final: 0.8276 (pt) REVERT: B 591 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8210 (tttp) REVERT: B 641 TYR cc_start: 0.8406 (m-10) cc_final: 0.7904 (m-80) REVERT: B 726 MET cc_start: 0.8170 (ptp) cc_final: 0.7922 (ptp) REVERT: B 924 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8198 (mmtt) REVERT: B 943 ILE cc_start: 0.8374 (mt) cc_final: 0.7973 (tp) REVERT: B 1013 MET cc_start: 0.4851 (tmm) cc_final: 0.3870 (tmm) REVERT: B 1057 MET cc_start: 0.8352 (mmm) cc_final: 0.7999 (ttm) REVERT: B 1134 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6432 (mtt90) REVERT: B 1151 ILE cc_start: 0.4794 (OUTLIER) cc_final: 0.4329 (pp) REVERT: B 1157 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6374 (mm-40) REVERT: B 1188 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6735 (mm-30) REVERT: C 278 GLU cc_start: 0.6798 (tp30) cc_final: 0.6500 (tp30) REVERT: C 327 TYR cc_start: 0.7948 (t80) cc_final: 0.7661 (t80) REVERT: E 11 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6211 (mtm-85) REVERT: E 122 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7177 (mttm) REVERT: F 85 MET cc_start: 0.8273 (ttm) cc_final: 0.7894 (mtt) REVERT: F 144 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 153 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (t) REVERT: G 21 LYS cc_start: 0.7515 (mttt) cc_final: 0.6794 (tmmt) REVERT: G 102 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7274 (tm-30) REVERT: G 134 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: H 16 ASP cc_start: 0.7100 (p0) cc_final: 0.6878 (p0) REVERT: H 33 GLN cc_start: 0.6161 (OUTLIER) cc_final: 0.5848 (mt0) REVERT: H 145 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6443 (ttm-80) REVERT: I 7 LEU cc_start: 0.6381 (mp) cc_final: 0.5688 (tp) REVERT: I 97 HIS cc_start: 0.0510 (t-90) cc_final: 0.0231 (t-90) REVERT: J 68 LYS cc_start: 0.6720 (tttp) cc_final: 0.5902 (mmtm) REVERT: K 91 TYR cc_start: 0.8340 (p90) cc_final: 0.8019 (p90) REVERT: L 42 ARG cc_start: 0.6109 (ptt-90) cc_final: 0.5647 (mmt-90) REVERT: N 36 LYS cc_start: 0.2733 (mmtt) cc_final: 0.1539 (ptpp) REVERT: N 80 MET cc_start: 0.3849 (ttp) cc_final: 0.3182 (tmm) REVERT: O 149 LYS cc_start: 0.7352 (ttpt) cc_final: 0.6940 (tttt) REVERT: O 151 TRP cc_start: 0.6695 (t-100) cc_final: 0.6311 (t-100) REVERT: O 182 MET cc_start: 0.6586 (ttt) cc_final: 0.6262 (ttt) REVERT: O 369 LYS cc_start: 0.8231 (ptpt) cc_final: 0.7739 (tmmt) REVERT: O 382 GLN cc_start: 0.7035 (pm20) cc_final: 0.6296 (mp10) REVERT: O 467 MET cc_start: 0.6425 (mmm) cc_final: 0.5572 (mmt) REVERT: O 486 PHE cc_start: 0.4705 (m-10) cc_final: 0.4045 (m-10) REVERT: O 541 PHE cc_start: 0.5717 (t80) cc_final: 0.5425 (t80) REVERT: O 583 GLN cc_start: 0.6893 (tp40) cc_final: 0.6648 (pm20) outliers start: 151 outliers final: 84 residues processed: 875 average time/residue: 0.6459 time to fit residues: 937.9732 Evaluate side-chains 743 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 649 time to evaluate : 5.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 382 GLU Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 514 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 551 optimal weight: 1.9990 chunk 419 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 266 optimal weight: 0.4980 chunk 375 optimal weight: 3.9990 chunk 560 optimal weight: 5.9990 chunk 593 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 531 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 294 HIS ** S 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 ASN R 223 ASN R 287 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1047 GLN ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 173 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 549 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 52042 Z= 0.225 Angle : 0.625 11.141 70656 Z= 0.327 Chirality : 0.045 0.330 7887 Planarity : 0.005 0.063 8789 Dihedral : 13.518 176.616 7523 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.89 % Favored : 92.10 % Rotamer: Outliers : 3.21 % Allowed : 13.32 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.10), residues: 6049 helix: -2.12 (0.10), residues: 2044 sheet: -2.55 (0.19), residues: 636 loop : -2.34 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 722 HIS 0.009 0.001 HIS B 532 PHE 0.025 0.002 PHE B 508 TYR 0.023 0.002 TYR B1098 ARG 0.007 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 682 time to evaluate : 5.669 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: Q 21 ARG cc_start: 0.0615 (pmt-80) cc_final: 0.0148 (tpp80) REVERT: Q 287 TRP cc_start: 0.1296 (t60) cc_final: 0.0829 (t60) REVERT: Q 292 GLU cc_start: 0.2256 (pm20) cc_final: 0.1652 (mp0) REVERT: Q 301 HIS cc_start: 0.4433 (m90) cc_final: 0.3293 (t-90) REVERT: S 221 ARG cc_start: 0.5433 (ttt90) cc_final: 0.3569 (ptt180) REVERT: S 386 MET cc_start: 0.3612 (tpp) cc_final: 0.3247 (mpp) REVERT: S 484 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.5543 (mtt180) REVERT: S 667 ASP cc_start: -0.1180 (t0) cc_final: -0.1440 (t0) REVERT: S 693 PHE cc_start: 0.0721 (m-80) cc_final: -0.0710 (p90) REVERT: S 772 ILE cc_start: 0.4061 (mm) cc_final: 0.3794 (pt) REVERT: S 777 MET cc_start: 0.1847 (ttp) cc_final: 0.0887 (tpp) REVERT: R 23 TYR cc_start: 0.1016 (t80) cc_final: 0.0762 (t80) REVERT: R 236 PHE cc_start: 0.3797 (t80) cc_final: 0.3510 (t80) REVERT: R 291 ARG cc_start: 0.3827 (mpt180) cc_final: 0.1855 (tpt-90) REVERT: R 307 LYS cc_start: 0.3278 (mmmt) cc_final: 0.2813 (tttm) REVERT: A 49 LEU cc_start: 0.7118 (mp) cc_final: 0.6733 (mt) REVERT: A 129 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6869 (pp) REVERT: A 236 CYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5307 (p) REVERT: A 347 ARG cc_start: 0.7014 (ptp90) cc_final: 0.5942 (ttt90) REVERT: A 420 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 509 GLU cc_start: 0.7563 (tp30) cc_final: 0.7108 (tp30) REVERT: A 601 MET cc_start: 0.8505 (mtm) cc_final: 0.7929 (mtm) REVERT: A 635 MET cc_start: 0.8042 (tmm) cc_final: 0.7713 (tmm) REVERT: A 693 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: A 785 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8130 (mm110) REVERT: A 953 GLU cc_start: 0.7819 (pt0) cc_final: 0.7153 (mm-30) REVERT: A 1012 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.2108 (ptmt) REVERT: A 1092 GLU cc_start: 0.7805 (mm-30) cc_final: 0.6960 (tm-30) REVERT: A 1245 ASP cc_start: 0.6878 (p0) cc_final: 0.5966 (m-30) REVERT: A 1315 ASN cc_start: 0.8151 (t0) cc_final: 0.7871 (t0) REVERT: A 1533 GLU cc_start: 0.6551 (pm20) cc_final: 0.6295 (tp30) REVERT: A 1535 PHE cc_start: 0.6602 (m-80) cc_final: 0.6295 (m-80) REVERT: A 1600 ARG cc_start: 0.7762 (mtm180) cc_final: 0.6647 (mtp-110) REVERT: A 1645 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7785 (mtpt) REVERT: B 229 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.5464 (t80) REVERT: B 268 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6690 (mm-30) REVERT: B 275 MET cc_start: 0.7470 (ttm) cc_final: 0.7178 (tpp) REVERT: B 441 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7377 (mttp) REVERT: B 444 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7892 (tpt170) REVERT: B 461 MET cc_start: 0.7483 (mmm) cc_final: 0.6246 (mmt) REVERT: B 495 ARG cc_start: 0.8062 (tpt90) cc_final: 0.7803 (tpt170) REVERT: B 519 LYS cc_start: 0.7668 (ttmt) cc_final: 0.6966 (mmtm) REVERT: B 550 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.6985 (ptt90) REVERT: B 588 ILE cc_start: 0.8654 (pt) cc_final: 0.8410 (pt) REVERT: B 591 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8179 (tttp) REVERT: B 641 TYR cc_start: 0.8524 (m-10) cc_final: 0.8060 (m-80) REVERT: B 726 MET cc_start: 0.8194 (ptp) cc_final: 0.7968 (ptp) REVERT: B 924 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8243 (mmtt) REVERT: B 943 ILE cc_start: 0.8449 (mt) cc_final: 0.8003 (tp) REVERT: B 1057 MET cc_start: 0.8395 (mmm) cc_final: 0.8011 (ttm) REVERT: B 1134 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6473 (mtt90) REVERT: B 1151 ILE cc_start: 0.4742 (OUTLIER) cc_final: 0.4345 (pp) REVERT: B 1157 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6306 (mm-40) REVERT: B 1188 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6696 (mm-30) REVERT: C 41 GLU cc_start: 0.6968 (mp0) cc_final: 0.6737 (mp0) REVERT: C 278 GLU cc_start: 0.6844 (tp30) cc_final: 0.6413 (tp30) REVERT: C 327 TYR cc_start: 0.8016 (t80) cc_final: 0.7663 (t80) REVERT: E 11 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6982 (tpp-160) REVERT: E 96 PHE cc_start: 0.6946 (t80) cc_final: 0.6722 (t80) REVERT: F 111 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7703 (pp) REVERT: F 144 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7476 (mt-10) REVERT: G 21 LYS cc_start: 0.7522 (mttt) cc_final: 0.6884 (tmmt) REVERT: G 85 GLU cc_start: 0.6858 (tt0) cc_final: 0.6282 (pp20) REVERT: G 102 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7362 (tm-30) REVERT: G 126 GLN cc_start: 0.7612 (tt0) cc_final: 0.7408 (tt0) REVERT: G 128 GLN cc_start: 0.8179 (mp10) cc_final: 0.7974 (mp10) REVERT: G 134 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5366 (tm-30) REVERT: G 138 PHE cc_start: 0.4685 (OUTLIER) cc_final: 0.4030 (t80) REVERT: H 9 ILE cc_start: 0.8681 (mt) cc_final: 0.8445 (mm) REVERT: H 145 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6400 (ttm-80) REVERT: I 97 HIS cc_start: 0.0691 (t-90) cc_final: 0.0351 (t-90) REVERT: J 2 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6927 (pp) REVERT: J 68 LYS cc_start: 0.7098 (tttp) cc_final: 0.5910 (mmtp) REVERT: K 81 MET cc_start: 0.8495 (mmm) cc_final: 0.8267 (mmm) REVERT: L 42 ARG cc_start: 0.6139 (ptt-90) cc_final: 0.5649 (mmt-90) REVERT: N 80 MET cc_start: 0.3936 (ttp) cc_final: 0.3096 (tmm) REVERT: N 166 LEU cc_start: 0.0941 (OUTLIER) cc_final: 0.0120 (pp) REVERT: N 178 GLU cc_start: 0.3104 (mp0) cc_final: 0.1660 (pm20) REVERT: O 149 LYS cc_start: 0.7369 (ttpt) cc_final: 0.6976 (tttt) REVERT: O 182 MET cc_start: 0.6721 (ttt) cc_final: 0.6342 (ttt) REVERT: O 369 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7692 (tmmt) REVERT: O 382 GLN cc_start: 0.7261 (pm20) cc_final: 0.6291 (mp10) REVERT: O 467 MET cc_start: 0.6493 (mmm) cc_final: 0.5527 (mmt) REVERT: O 486 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.4350 (m-10) REVERT: O 541 PHE cc_start: 0.5778 (t80) cc_final: 0.5430 (t80) outliers start: 176 outliers final: 111 residues processed: 796 average time/residue: 0.6244 time to fit residues: 830.1895 Evaluate side-chains 746 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 620 time to evaluate : 5.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 382 GLU Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1605 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 215 LEU Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 343 VAL Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 434 LEU Chi-restraints excluded: chain O residue 486 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 494 optimal weight: 2.9990 chunk 336 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 441 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 506 optimal weight: 4.9990 chunk 410 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 532 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 HIS S 554 ASN S 758 ASN R 223 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 433 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 52042 Z= 0.155 Angle : 0.573 14.477 70656 Z= 0.298 Chirality : 0.043 0.223 7887 Planarity : 0.004 0.059 8789 Dihedral : 13.386 179.379 7523 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 3.43 % Allowed : 13.90 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.10), residues: 6049 helix: -1.70 (0.11), residues: 2032 sheet: -2.37 (0.19), residues: 649 loop : -2.18 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 143 HIS 0.009 0.001 HIS Q 171 PHE 0.017 0.001 PHE A 437 TYR 0.023 0.001 TYR R 208 ARG 0.005 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 684 time to evaluate : 5.662 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: Q 21 ARG cc_start: 0.0744 (OUTLIER) cc_final: 0.0255 (tpp80) REVERT: Q 238 HIS cc_start: 0.4970 (m90) cc_final: 0.4650 (m-70) REVERT: Q 287 TRP cc_start: 0.1209 (t60) cc_final: 0.0753 (t60) REVERT: Q 292 GLU cc_start: 0.2244 (pm20) cc_final: 0.1627 (mp0) REVERT: Q 301 HIS cc_start: 0.4433 (m90) cc_final: 0.3324 (t-90) REVERT: Q 366 TYR cc_start: 0.6065 (p90) cc_final: 0.5818 (p90) REVERT: S 386 MET cc_start: 0.3710 (tpp) cc_final: 0.3249 (mpp) REVERT: S 471 MET cc_start: -0.0209 (tpp) cc_final: -0.1196 (tmm) REVERT: S 484 ARG cc_start: 0.6831 (mmm-85) cc_final: 0.5785 (mtt180) REVERT: S 667 ASP cc_start: -0.1245 (t0) cc_final: -0.1511 (t0) REVERT: S 693 PHE cc_start: 0.0712 (m-80) cc_final: -0.0747 (p90) REVERT: R 23 TYR cc_start: 0.0864 (t80) cc_final: 0.0577 (t80) REVERT: R 236 PHE cc_start: 0.3810 (t80) cc_final: 0.3403 (t80) REVERT: R 287 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.5923 (t0) REVERT: R 291 ARG cc_start: 0.3793 (mpt180) cc_final: 0.1754 (tmt-80) REVERT: R 302 ARG cc_start: 0.4440 (mtt-85) cc_final: 0.4182 (ptp-170) REVERT: R 307 LYS cc_start: 0.3138 (mmmt) cc_final: 0.2763 (tttm) REVERT: R 398 ASP cc_start: 0.4987 (t0) cc_final: 0.4760 (m-30) REVERT: A 129 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6865 (pp) REVERT: A 347 ARG cc_start: 0.7001 (ptp90) cc_final: 0.5914 (ttt90) REVERT: A 420 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 424 MET cc_start: 0.6970 (mmp) cc_final: 0.5758 (ptm) REVERT: A 509 GLU cc_start: 0.7660 (tp30) cc_final: 0.7333 (tt0) REVERT: A 601 MET cc_start: 0.8485 (mtm) cc_final: 0.8150 (mtm) REVERT: A 633 MET cc_start: 0.8012 (mtt) cc_final: 0.7737 (ttm) REVERT: A 693 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: A 785 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7942 (mm110) REVERT: A 953 GLU cc_start: 0.7778 (pt0) cc_final: 0.7557 (mm-30) REVERT: A 1012 LYS cc_start: 0.3331 (OUTLIER) cc_final: 0.1948 (ptmt) REVERT: A 1020 GLN cc_start: 0.7501 (tp40) cc_final: 0.7294 (tp40) REVERT: A 1092 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6905 (tm-30) REVERT: A 1315 ASN cc_start: 0.8097 (t0) cc_final: 0.7837 (t0) REVERT: A 1535 PHE cc_start: 0.6547 (m-80) cc_final: 0.6276 (m-80) REVERT: A 1600 ARG cc_start: 0.7591 (mtm180) cc_final: 0.6482 (mtp-110) REVERT: A 1627 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7528 (mt) REVERT: A 1645 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7732 (mtpt) REVERT: B 43 GLN cc_start: 0.7891 (tp40) cc_final: 0.7218 (tt0) REVERT: B 229 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.5383 (t80) REVERT: B 261 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.8080 (ttp-170) REVERT: B 335 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6602 (ttp-110) REVERT: B 441 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7388 (mttp) REVERT: B 550 ARG cc_start: 0.7627 (mmt-90) cc_final: 0.7045 (ptt90) REVERT: B 588 ILE cc_start: 0.8585 (pt) cc_final: 0.8318 (pt) REVERT: B 641 TYR cc_start: 0.8430 (m-10) cc_final: 0.7916 (m-80) REVERT: B 726 MET cc_start: 0.8027 (ptp) cc_final: 0.7793 (ptp) REVERT: B 861 TYR cc_start: 0.7631 (p90) cc_final: 0.7152 (p90) REVERT: B 924 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8252 (mmtt) REVERT: B 943 ILE cc_start: 0.8449 (mt) cc_final: 0.8064 (tp) REVERT: B 970 LYS cc_start: 0.5434 (pttt) cc_final: 0.5206 (mmmt) REVERT: B 1057 MET cc_start: 0.8346 (mmm) cc_final: 0.7996 (ttm) REVERT: B 1134 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6493 (mtt90) REVERT: B 1151 ILE cc_start: 0.5178 (OUTLIER) cc_final: 0.4899 (pp) REVERT: B 1157 GLN cc_start: 0.6590 (mm-40) cc_final: 0.6362 (mm-40) REVERT: B 1188 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6587 (mm-30) REVERT: C 278 GLU cc_start: 0.6831 (tp30) cc_final: 0.6399 (tp30) REVERT: C 327 TYR cc_start: 0.7909 (t80) cc_final: 0.7630 (t80) REVERT: E 11 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6988 (tpp-160) REVERT: E 96 PHE cc_start: 0.6929 (t80) cc_final: 0.6236 (t80) REVERT: F 111 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7830 (pp) REVERT: G 21 LYS cc_start: 0.7526 (mttt) cc_final: 0.6929 (tmmt) REVERT: G 87 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8483 (tt) REVERT: G 110 ASP cc_start: 0.6923 (m-30) cc_final: 0.6603 (t0) REVERT: G 134 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5475 (tm-30) REVERT: H 145 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6384 (ttm-80) REVERT: J 2 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6743 (pp) REVERT: J 68 LYS cc_start: 0.6919 (tttp) cc_final: 0.5881 (mmtm) REVERT: K 81 MET cc_start: 0.8429 (mmm) cc_final: 0.8215 (mmm) REVERT: K 91 TYR cc_start: 0.8331 (p90) cc_final: 0.8126 (p90) REVERT: L 42 ARG cc_start: 0.6069 (ptt-90) cc_final: 0.5574 (mmt-90) REVERT: N 80 MET cc_start: 0.3997 (ttp) cc_final: 0.3157 (tmm) REVERT: N 107 MET cc_start: 0.4730 (mmm) cc_final: 0.3569 (mmm) REVERT: N 153 VAL cc_start: 0.6102 (OUTLIER) cc_final: 0.5667 (m) REVERT: N 166 LEU cc_start: 0.1119 (OUTLIER) cc_final: 0.0514 (pp) REVERT: N 178 GLU cc_start: 0.3026 (mp0) cc_final: 0.1667 (pm20) REVERT: O 149 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6984 (tttt) REVERT: O 369 LYS cc_start: 0.8196 (ptpt) cc_final: 0.7767 (tmmt) REVERT: O 382 GLN cc_start: 0.7046 (pm20) cc_final: 0.6350 (mp10) REVERT: O 451 ASN cc_start: 0.5571 (m-40) cc_final: 0.4746 (p0) REVERT: O 452 ARG cc_start: 0.5477 (tpm170) cc_final: 0.5180 (tpm170) REVERT: O 467 MET cc_start: 0.6430 (mmm) cc_final: 0.5531 (mmt) REVERT: O 486 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.4111 (m-10) REVERT: O 509 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6463 (mtt) REVERT: O 541 PHE cc_start: 0.5787 (t80) cc_final: 0.5466 (t80) outliers start: 188 outliers final: 96 residues processed: 818 average time/residue: 0.5499 time to fit residues: 753.5004 Evaluate side-chains 725 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 610 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 351 SER Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 366 THR Chi-restraints excluded: chain O residue 434 LEU Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain O residue 509 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 199 optimal weight: 0.9980 chunk 534 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 594 optimal weight: 1.9990 chunk 493 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 196 optimal weight: 0.9990 chunk 311 optimal weight: 0.2980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52042 Z= 0.184 Angle : 0.590 12.092 70656 Z= 0.305 Chirality : 0.043 0.226 7887 Planarity : 0.004 0.059 8789 Dihedral : 13.293 176.140 7523 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 3.25 % Allowed : 14.87 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 6049 helix: -1.46 (0.11), residues: 2046 sheet: -2.37 (0.20), residues: 643 loop : -2.11 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 316 HIS 0.007 0.001 HIS B 532 PHE 0.018 0.001 PHE A1472 TYR 0.025 0.001 TYR B 317 ARG 0.007 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 661 time to evaluate : 4.366 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: Q 21 ARG cc_start: 0.0839 (OUTLIER) cc_final: 0.0320 (tpp80) REVERT: Q 158 MET cc_start: 0.0456 (OUTLIER) cc_final: 0.0165 (mpp) REVERT: Q 238 HIS cc_start: 0.4993 (m90) cc_final: 0.4761 (m-70) REVERT: Q 287 TRP cc_start: 0.1049 (t60) cc_final: 0.0647 (t60) REVERT: Q 292 GLU cc_start: 0.2296 (pm20) cc_final: 0.1661 (mp0) REVERT: Q 301 HIS cc_start: 0.4434 (m90) cc_final: 0.3296 (t-90) REVERT: S 386 MET cc_start: 0.3641 (tpp) cc_final: 0.3136 (mpp) REVERT: S 484 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.5726 (mtt180) REVERT: S 667 ASP cc_start: -0.0732 (t0) cc_final: -0.1034 (t0) REVERT: S 693 PHE cc_start: 0.0675 (m-80) cc_final: -0.0760 (p90) REVERT: S 777 MET cc_start: 0.2078 (ttp) cc_final: 0.1671 (ptp) REVERT: R 23 TYR cc_start: 0.0871 (t80) cc_final: 0.0597 (t80) REVERT: R 287 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6398 (t0) REVERT: R 291 ARG cc_start: 0.3641 (mpt180) cc_final: 0.1701 (tmt-80) REVERT: R 398 ASP cc_start: 0.5245 (t0) cc_final: 0.4894 (m-30) REVERT: M 103 LYS cc_start: 0.4697 (mmtt) cc_final: 0.4472 (mmmt) REVERT: A 49 LEU cc_start: 0.6923 (mp) cc_final: 0.6569 (mt) REVERT: A 129 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6853 (pp) REVERT: A 238 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6183 (ppp) REVERT: A 347 ARG cc_start: 0.7046 (ptp90) cc_final: 0.5995 (ttt90) REVERT: A 420 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6671 (t80) REVERT: A 491 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 509 GLU cc_start: 0.7615 (tp30) cc_final: 0.7349 (tt0) REVERT: A 693 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 785 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8020 (mm110) REVERT: A 928 MET cc_start: 0.8655 (ptp) cc_final: 0.8439 (ptp) REVERT: A 953 GLU cc_start: 0.8121 (pt0) cc_final: 0.7407 (mm-30) REVERT: A 1012 LYS cc_start: 0.3399 (OUTLIER) cc_final: 0.1854 (ptmt) REVERT: A 1092 GLU cc_start: 0.7773 (mm-30) cc_final: 0.6878 (tm-30) REVERT: A 1315 ASN cc_start: 0.8163 (t0) cc_final: 0.7911 (t0) REVERT: A 1535 PHE cc_start: 0.6629 (m-80) cc_final: 0.6314 (m-80) REVERT: A 1600 ARG cc_start: 0.7586 (mtm180) cc_final: 0.7286 (ptp-170) REVERT: A 1601 GLN cc_start: 0.7904 (mp10) cc_final: 0.7545 (mt0) REVERT: A 1645 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7667 (mtpt) REVERT: B 43 GLN cc_start: 0.7921 (tp40) cc_final: 0.7217 (tt0) REVERT: B 201 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7521 (mttt) REVERT: B 229 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.5418 (t80) REVERT: B 261 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.7981 (ttp-170) REVERT: B 317 TYR cc_start: 0.6648 (m-10) cc_final: 0.6368 (m-10) REVERT: B 335 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6608 (ttp-110) REVERT: B 441 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7311 (mttp) REVERT: B 550 ARG cc_start: 0.7629 (mmt-90) cc_final: 0.7048 (ptt90) REVERT: B 588 ILE cc_start: 0.8651 (pt) cc_final: 0.8391 (pt) REVERT: B 641 TYR cc_start: 0.8411 (m-10) cc_final: 0.7857 (m-80) REVERT: B 726 MET cc_start: 0.7970 (ptp) cc_final: 0.7742 (ptp) REVERT: B 861 TYR cc_start: 0.7661 (p90) cc_final: 0.7267 (p90) REVERT: B 924 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8263 (mmtt) REVERT: B 943 ILE cc_start: 0.8514 (mt) cc_final: 0.8071 (tp) REVERT: B 985 ILE cc_start: 0.2364 (OUTLIER) cc_final: 0.2005 (mm) REVERT: B 1057 MET cc_start: 0.8354 (mmm) cc_final: 0.8016 (ttm) REVERT: B 1134 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6450 (mtt90) REVERT: B 1151 ILE cc_start: 0.5115 (OUTLIER) cc_final: 0.4813 (pp) REVERT: B 1157 GLN cc_start: 0.6620 (mm-40) cc_final: 0.6396 (mm-40) REVERT: B 1188 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6523 (mm-30) REVERT: C 278 GLU cc_start: 0.6807 (tp30) cc_final: 0.6371 (tp30) REVERT: C 327 TYR cc_start: 0.7931 (t80) cc_final: 0.7693 (t80) REVERT: E 11 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7003 (tpp-160) REVERT: E 30 ILE cc_start: 0.8061 (mm) cc_final: 0.7843 (mm) REVERT: E 96 PHE cc_start: 0.6897 (t80) cc_final: 0.6215 (t80) REVERT: F 111 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7878 (pp) REVERT: G 21 LYS cc_start: 0.7478 (mttt) cc_final: 0.6941 (tmmt) REVERT: G 85 GLU cc_start: 0.6813 (tt0) cc_final: 0.6317 (pp20) REVERT: G 87 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8531 (tt) REVERT: G 110 ASP cc_start: 0.7091 (m-30) cc_final: 0.6766 (t0) REVERT: G 128 GLN cc_start: 0.8119 (mp10) cc_final: 0.7677 (mp10) REVERT: G 134 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5405 (tm-30) REVERT: H 9 ILE cc_start: 0.8715 (mt) cc_final: 0.8485 (mm) REVERT: H 145 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.6421 (ttm-80) REVERT: J 2 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6865 (pp) REVERT: J 68 LYS cc_start: 0.7312 (tttp) cc_final: 0.5942 (mmtm) REVERT: K 85 ASP cc_start: 0.8042 (t0) cc_final: 0.7318 (t0) REVERT: K 91 TYR cc_start: 0.8307 (p90) cc_final: 0.7994 (p90) REVERT: L 42 ARG cc_start: 0.6019 (ptt-90) cc_final: 0.5574 (mmt-90) REVERT: N 80 MET cc_start: 0.4014 (ttp) cc_final: 0.3138 (tmm) REVERT: N 107 MET cc_start: 0.4905 (mmm) cc_final: 0.3790 (mmm) REVERT: N 166 LEU cc_start: 0.1122 (OUTLIER) cc_final: 0.0514 (pp) REVERT: N 178 GLU cc_start: 0.3080 (mp0) cc_final: 0.1686 (pm20) REVERT: O 149 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6886 (tttt) REVERT: O 369 LYS cc_start: 0.8102 (ptpt) cc_final: 0.7778 (tmmt) REVERT: O 382 GLN cc_start: 0.7158 (pm20) cc_final: 0.6318 (mp10) REVERT: O 451 ASN cc_start: 0.5548 (m-40) cc_final: 0.4845 (p0) REVERT: O 452 ARG cc_start: 0.5472 (tpm170) cc_final: 0.5147 (tpm170) REVERT: O 467 MET cc_start: 0.6672 (mmm) cc_final: 0.5903 (mmt) REVERT: O 486 PHE cc_start: 0.4943 (OUTLIER) cc_final: 0.4076 (m-10) REVERT: O 541 PHE cc_start: 0.5845 (t80) cc_final: 0.5518 (t80) outliers start: 178 outliers final: 126 residues processed: 781 average time/residue: 0.5822 time to fit residues: 762.3318 Evaluate side-chains 760 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 615 time to evaluate : 6.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 419 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 467 PHE Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 154 ARG Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 215 LEU Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 366 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 434 LEU Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain O residue 509 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 572 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 433 optimal weight: 2.9990 chunk 336 optimal weight: 0.6980 chunk 500 optimal weight: 0.6980 chunk 331 optimal weight: 0.9980 chunk 591 optimal weight: 3.9990 chunk 370 optimal weight: 2.9990 chunk 360 optimal weight: 0.0670 chunk 273 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 ASN S 267 ASN S 487 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN B1041 ASN ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 52042 Z= 0.156 Angle : 0.566 11.559 70656 Z= 0.291 Chirality : 0.042 0.243 7887 Planarity : 0.004 0.085 8789 Dihedral : 13.193 175.222 7523 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.56 % Favored : 93.42 % Rotamer: Outliers : 3.08 % Allowed : 15.34 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6049 helix: -1.25 (0.11), residues: 2053 sheet: -2.21 (0.20), residues: 645 loop : -2.00 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 314 HIS 0.005 0.001 HIS B 532 PHE 0.018 0.001 PHE A 437 TYR 0.025 0.001 TYR B 317 ARG 0.015 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 651 time to evaluate : 5.879 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: Q 21 ARG cc_start: 0.0863 (OUTLIER) cc_final: 0.0316 (tpp80) REVERT: Q 108 PHE cc_start: 0.0383 (OUTLIER) cc_final: 0.0082 (t80) REVERT: Q 287 TRP cc_start: 0.1027 (t60) cc_final: 0.0599 (t60) REVERT: Q 292 GLU cc_start: 0.2334 (pm20) cc_final: 0.1714 (mp0) REVERT: Q 301 HIS cc_start: 0.4498 (m90) cc_final: 0.3401 (t-90) REVERT: S 386 MET cc_start: 0.3599 (tpp) cc_final: 0.3101 (mpp) REVERT: S 471 MET cc_start: 0.0365 (tpp) cc_final: -0.1175 (tmm) REVERT: S 484 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.5667 (mtt180) REVERT: S 667 ASP cc_start: -0.0613 (t0) cc_final: -0.0885 (t0) REVERT: S 693 PHE cc_start: 0.0589 (m-80) cc_final: -0.0794 (p90) REVERT: S 694 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.4804 (mp) REVERT: S 777 MET cc_start: 0.2191 (ttp) cc_final: 0.1758 (ptp) REVERT: R 23 TYR cc_start: 0.0739 (t80) cc_final: 0.0484 (t80) REVERT: R 283 ARG cc_start: 0.4502 (ttp-170) cc_final: 0.4245 (ttp80) REVERT: R 287 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6407 (t0) REVERT: R 291 ARG cc_start: 0.3580 (mpt180) cc_final: 0.1575 (tmt-80) REVERT: R 302 ARG cc_start: 0.4602 (mtt-85) cc_final: 0.3247 (ptm-80) REVERT: A 238 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5262 (ppp) REVERT: A 347 ARG cc_start: 0.7047 (ptp90) cc_final: 0.5971 (ttt90) REVERT: A 420 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 424 MET cc_start: 0.6745 (mmp) cc_final: 0.5539 (ptm) REVERT: A 439 ASP cc_start: 0.7010 (m-30) cc_final: 0.6406 (p0) REVERT: A 491 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 509 GLU cc_start: 0.7600 (tp30) cc_final: 0.7335 (tt0) REVERT: A 693 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: A 785 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8075 (mm-40) REVERT: A 937 ASN cc_start: 0.7006 (m110) cc_final: 0.6481 (m110) REVERT: A 953 GLU cc_start: 0.8083 (pt0) cc_final: 0.7376 (mm-30) REVERT: A 1012 LYS cc_start: 0.3240 (OUTLIER) cc_final: 0.1795 (ptmt) REVERT: A 1020 GLN cc_start: 0.7506 (tp40) cc_final: 0.7304 (tp40) REVERT: A 1245 ASP cc_start: 0.7023 (p0) cc_final: 0.5905 (m-30) REVERT: A 1315 ASN cc_start: 0.8133 (t0) cc_final: 0.7908 (t0) REVERT: A 1535 PHE cc_start: 0.6635 (m-80) cc_final: 0.6389 (m-80) REVERT: A 1601 GLN cc_start: 0.7905 (mp10) cc_final: 0.7444 (mt0) REVERT: A 1645 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7705 (mtpt) REVERT: B 43 GLN cc_start: 0.7895 (tp40) cc_final: 0.7221 (tt0) REVERT: B 201 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7462 (mttt) REVERT: B 229 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.5453 (t80) REVERT: B 261 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.7928 (ttp-170) REVERT: B 335 ARG cc_start: 0.7151 (ttt90) cc_final: 0.6559 (ttp-110) REVERT: B 441 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7272 (mttm) REVERT: B 550 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.6956 (ptt90) REVERT: B 588 ILE cc_start: 0.8650 (pt) cc_final: 0.8380 (pt) REVERT: B 641 TYR cc_start: 0.8390 (m-10) cc_final: 0.7825 (m-80) REVERT: B 726 MET cc_start: 0.7867 (ptp) cc_final: 0.7631 (ptp) REVERT: B 924 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8251 (mmtt) REVERT: B 940 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5496 (tp30) REVERT: B 943 ILE cc_start: 0.8485 (mt) cc_final: 0.8086 (tp) REVERT: B 970 LYS cc_start: 0.5792 (pttt) cc_final: 0.5221 (mmmt) REVERT: B 977 ILE cc_start: 0.1908 (OUTLIER) cc_final: 0.1696 (mt) REVERT: B 1057 MET cc_start: 0.8374 (mmm) cc_final: 0.8041 (ttm) REVERT: B 1134 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6463 (mtt90) REVERT: B 1151 ILE cc_start: 0.5143 (OUTLIER) cc_final: 0.4888 (pp) REVERT: B 1188 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6450 (mm-30) REVERT: C 278 GLU cc_start: 0.6770 (tp30) cc_final: 0.6341 (tp30) REVERT: E 11 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6829 (tpp-160) REVERT: E 30 ILE cc_start: 0.8021 (mm) cc_final: 0.7805 (mm) REVERT: E 96 PHE cc_start: 0.6885 (t80) cc_final: 0.6189 (t80) REVERT: F 111 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7926 (pp) REVERT: G 21 LYS cc_start: 0.7490 (mttt) cc_final: 0.6978 (tmmt) REVERT: G 85 GLU cc_start: 0.6851 (tt0) cc_final: 0.6241 (pp20) REVERT: G 128 GLN cc_start: 0.8031 (mp10) cc_final: 0.7612 (mp10) REVERT: G 134 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5315 (tm-30) REVERT: H 9 ILE cc_start: 0.8707 (mt) cc_final: 0.8480 (mm) REVERT: H 145 ARG cc_start: 0.6914 (ttp-110) cc_final: 0.6342 (ttm-80) REVERT: J 2 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6775 (pp) REVERT: J 68 LYS cc_start: 0.7385 (tttp) cc_final: 0.5905 (mmtm) REVERT: K 85 ASP cc_start: 0.8064 (t0) cc_final: 0.7364 (t0) REVERT: K 91 TYR cc_start: 0.8297 (p90) cc_final: 0.7986 (p90) REVERT: L 42 ARG cc_start: 0.6027 (ptt-90) cc_final: 0.5650 (mmt-90) REVERT: N 80 MET cc_start: 0.4198 (ttp) cc_final: 0.3127 (tmm) REVERT: N 107 MET cc_start: 0.4805 (mmm) cc_final: 0.3741 (mmm) REVERT: N 166 LEU cc_start: 0.0930 (OUTLIER) cc_final: 0.0479 (pp) REVERT: N 178 GLU cc_start: 0.3271 (mp0) cc_final: 0.1812 (pm20) REVERT: O 149 LYS cc_start: 0.7202 (ttpt) cc_final: 0.6861 (tttt) REVERT: O 369 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7755 (tmmt) REVERT: O 382 GLN cc_start: 0.7149 (pm20) cc_final: 0.6296 (mp10) REVERT: O 451 ASN cc_start: 0.5379 (m-40) cc_final: 0.4720 (p0) REVERT: O 452 ARG cc_start: 0.5304 (tpm170) cc_final: 0.5035 (tpm170) REVERT: O 467 MET cc_start: 0.6691 (mmm) cc_final: 0.5934 (mmt) REVERT: O 541 PHE cc_start: 0.5871 (t80) cc_final: 0.5559 (t80) outliers start: 169 outliers final: 109 residues processed: 765 average time/residue: 0.6159 time to fit residues: 792.7140 Evaluate side-chains 731 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 604 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 108 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 467 PHE Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 940 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 996 PHE Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 351 SER Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 509 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 366 optimal weight: 0.0470 chunk 236 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 0.0980 chunk 376 optimal weight: 0.0000 chunk 403 optimal weight: 0.6980 chunk 292 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 465 optimal weight: 3.9990 overall best weight: 0.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 425 HIS ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 52042 Z= 0.138 Angle : 0.561 11.548 70656 Z= 0.287 Chirality : 0.042 0.196 7887 Planarity : 0.004 0.063 8789 Dihedral : 13.092 173.909 7518 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.23 % Favored : 93.75 % Rotamer: Outliers : 2.39 % Allowed : 16.36 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.10), residues: 6049 helix: -1.01 (0.11), residues: 2059 sheet: -2.07 (0.20), residues: 633 loop : -1.90 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP R 314 HIS 0.004 0.001 HIS L 53 PHE 0.020 0.001 PHE A 437 TYR 0.036 0.001 TYR B 317 ARG 0.009 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 670 time to evaluate : 5.697 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: Q 21 ARG cc_start: 0.0922 (OUTLIER) cc_final: 0.0440 (tpp80) REVERT: Q 108 PHE cc_start: 0.0434 (OUTLIER) cc_final: 0.0179 (t80) REVERT: Q 158 MET cc_start: -0.0801 (mmp) cc_final: -0.1118 (mmp) REVERT: Q 287 TRP cc_start: 0.0997 (t60) cc_final: 0.0588 (t60) REVERT: Q 292 GLU cc_start: 0.2539 (pm20) cc_final: 0.1919 (mp0) REVERT: Q 301 HIS cc_start: 0.4520 (m90) cc_final: 0.3385 (t-90) REVERT: S 386 MET cc_start: 0.3609 (tpp) cc_final: 0.3286 (tpp) REVERT: S 471 MET cc_start: 0.0208 (tpp) cc_final: -0.1104 (tmm) REVERT: S 484 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.5807 (mtt180) REVERT: S 667 ASP cc_start: -0.0651 (t0) cc_final: -0.0950 (t0) REVERT: S 693 PHE cc_start: 0.0448 (m-80) cc_final: -0.0883 (p90) REVERT: S 777 MET cc_start: 0.2221 (ttp) cc_final: 0.2012 (ptp) REVERT: R 23 TYR cc_start: 0.0577 (t80) cc_final: 0.0372 (t80) REVERT: R 283 ARG cc_start: 0.4317 (ttp-170) cc_final: 0.4070 (ttp80) REVERT: R 287 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6386 (t0) REVERT: R 290 TYR cc_start: 0.3948 (m-80) cc_final: 0.3410 (m-80) REVERT: R 291 ARG cc_start: 0.3648 (mpt180) cc_final: 0.1575 (tmt-80) REVERT: R 302 ARG cc_start: 0.4502 (mtt-85) cc_final: 0.3176 (ptm-80) REVERT: R 398 ASP cc_start: 0.4997 (t0) cc_final: 0.4738 (m-30) REVERT: A 238 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.5089 (ppp) REVERT: A 347 ARG cc_start: 0.6955 (ptp90) cc_final: 0.5904 (ttt90) REVERT: A 420 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6464 (t80) REVERT: A 424 MET cc_start: 0.6692 (mmp) cc_final: 0.5664 (ptm) REVERT: A 439 ASP cc_start: 0.6924 (m-30) cc_final: 0.6344 (p0) REVERT: A 491 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6657 (mm-30) REVERT: A 509 GLU cc_start: 0.7593 (tp30) cc_final: 0.7315 (tt0) REVERT: A 693 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: A 785 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8059 (mm-40) REVERT: A 874 GLU cc_start: 0.7801 (tm-30) cc_final: 0.6858 (pt0) REVERT: A 891 ILE cc_start: 0.8587 (mm) cc_final: 0.8382 (mp) REVERT: A 937 ASN cc_start: 0.6822 (m110) cc_final: 0.6285 (m110) REVERT: A 953 GLU cc_start: 0.8081 (pt0) cc_final: 0.7405 (mm-30) REVERT: A 1012 LYS cc_start: 0.3230 (OUTLIER) cc_final: 0.1898 (ptmt) REVERT: A 1092 GLU cc_start: 0.7824 (mm-30) cc_final: 0.6929 (tm-30) REVERT: A 1245 ASP cc_start: 0.7044 (p0) cc_final: 0.6057 (m-30) REVERT: A 1645 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7639 (mtpt) REVERT: B 43 GLN cc_start: 0.7876 (tp40) cc_final: 0.7287 (tt0) REVERT: B 201 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7374 (mttt) REVERT: B 229 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.5372 (t80) REVERT: B 261 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7963 (ttp-170) REVERT: B 335 ARG cc_start: 0.6975 (ttt90) cc_final: 0.6562 (ttp-110) REVERT: B 441 LYS cc_start: 0.7534 (mtmm) cc_final: 0.7208 (mttm) REVERT: B 550 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.6967 (ptt90) REVERT: B 588 ILE cc_start: 0.8635 (pt) cc_final: 0.8364 (pt) REVERT: B 641 TYR cc_start: 0.8347 (m-10) cc_final: 0.7747 (m-80) REVERT: B 690 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: B 726 MET cc_start: 0.7817 (ptp) cc_final: 0.7598 (ptp) REVERT: B 924 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8207 (mmtt) REVERT: B 940 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5527 (tp30) REVERT: B 943 ILE cc_start: 0.8474 (mt) cc_final: 0.8048 (tp) REVERT: B 1057 MET cc_start: 0.8362 (mmm) cc_final: 0.8046 (ttm) REVERT: B 1151 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4768 (pp) REVERT: B 1188 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6465 (mm-30) REVERT: C 278 GLU cc_start: 0.6728 (tp30) cc_final: 0.6343 (tp30) REVERT: E 11 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6985 (tpp-160) REVERT: E 30 ILE cc_start: 0.7988 (mm) cc_final: 0.7666 (mm) REVERT: E 96 PHE cc_start: 0.6843 (t80) cc_final: 0.6157 (t80) REVERT: F 111 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7931 (pp) REVERT: G 21 LYS cc_start: 0.7402 (mttt) cc_final: 0.6972 (tmmt) REVERT: G 110 ASP cc_start: 0.6971 (m-30) cc_final: 0.6694 (t0) REVERT: G 128 GLN cc_start: 0.8054 (mp10) cc_final: 0.7809 (mp10) REVERT: G 134 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5221 (tm-30) REVERT: H 9 ILE cc_start: 0.8708 (mt) cc_final: 0.8475 (mm) REVERT: H 145 ARG cc_start: 0.6935 (ttp-110) cc_final: 0.6344 (ttm-80) REVERT: I 41 GLN cc_start: 0.6154 (tp-100) cc_final: 0.5872 (tt0) REVERT: J 68 LYS cc_start: 0.7306 (tttp) cc_final: 0.5872 (mmtm) REVERT: K 85 ASP cc_start: 0.7843 (t0) cc_final: 0.7562 (t0) REVERT: K 91 TYR cc_start: 0.8242 (p90) cc_final: 0.7992 (p90) REVERT: L 42 ARG cc_start: 0.5948 (ptt-90) cc_final: 0.5618 (mmt-90) REVERT: N 80 MET cc_start: 0.4112 (ttp) cc_final: 0.3033 (tmm) REVERT: N 107 MET cc_start: 0.4807 (mmm) cc_final: 0.3281 (mmm) REVERT: N 166 LEU cc_start: 0.0892 (OUTLIER) cc_final: 0.0507 (pp) REVERT: O 149 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6807 (tttt) REVERT: O 151 TRP cc_start: 0.6898 (t-100) cc_final: 0.6236 (t-100) REVERT: O 369 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7811 (tmmt) REVERT: O 382 GLN cc_start: 0.7101 (pm20) cc_final: 0.6287 (mp10) REVERT: O 451 ASN cc_start: 0.5210 (m-40) cc_final: 0.4770 (p0) REVERT: O 452 ARG cc_start: 0.5340 (tpm170) cc_final: 0.5124 (tpm170) REVERT: O 467 MET cc_start: 0.6624 (mmm) cc_final: 0.5914 (mmt) REVERT: O 541 PHE cc_start: 0.5860 (t80) cc_final: 0.5569 (t80) REVERT: O 612 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6068 (tp30) outliers start: 131 outliers final: 92 residues processed: 758 average time/residue: 0.6214 time to fit residues: 790.6811 Evaluate side-chains 713 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 606 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 108 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 382 GLU Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 940 GLU Chi-restraints excluded: chain B residue 996 PHE Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 509 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 538 optimal weight: 0.0870 chunk 566 optimal weight: 0.0980 chunk 517 optimal weight: 0.3980 chunk 551 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 433 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 498 optimal weight: 5.9990 chunk 521 optimal weight: 4.9990 chunk 549 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 425 HIS ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 52042 Z= 0.149 Angle : 0.563 12.047 70656 Z= 0.288 Chirality : 0.042 0.193 7887 Planarity : 0.004 0.064 8789 Dihedral : 13.054 172.799 7516 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.64 % Rotamer: Outliers : 2.43 % Allowed : 16.69 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 6049 helix: -0.87 (0.11), residues: 2062 sheet: -2.02 (0.20), residues: 623 loop : -1.83 (0.11), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 314 HIS 0.004 0.001 HIS I 97 PHE 0.025 0.001 PHE B 376 TYR 0.036 0.001 TYR B 317 ARG 0.014 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12098 Ramachandran restraints generated. 6049 Oldfield, 0 Emsley, 6049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 628 time to evaluate : 5.639 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: Q 21 ARG cc_start: 0.0987 (OUTLIER) cc_final: 0.0445 (tpp80) REVERT: Q 108 PHE cc_start: 0.0456 (OUTLIER) cc_final: 0.0174 (t80) REVERT: Q 158 MET cc_start: -0.0763 (mmp) cc_final: -0.1067 (mmp) REVERT: Q 287 TRP cc_start: 0.1023 (t60) cc_final: 0.0608 (t60) REVERT: Q 292 GLU cc_start: 0.2567 (pm20) cc_final: 0.1952 (mp0) REVERT: Q 301 HIS cc_start: 0.4494 (m90) cc_final: 0.3399 (t-90) REVERT: S 386 MET cc_start: 0.3680 (tpp) cc_final: 0.3328 (tpp) REVERT: S 471 MET cc_start: 0.0115 (tpp) cc_final: -0.1191 (tmm) REVERT: S 484 ARG cc_start: 0.6811 (mmm-85) cc_final: 0.5746 (mtt180) REVERT: S 667 ASP cc_start: -0.0624 (t0) cc_final: -0.0900 (t0) REVERT: S 693 PHE cc_start: 0.0240 (m-80) cc_final: -0.1062 (p90) REVERT: R 287 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6448 (t0) REVERT: R 291 ARG cc_start: 0.3564 (mpt180) cc_final: 0.1465 (tmt-80) REVERT: R 302 ARG cc_start: 0.4610 (mtt-85) cc_final: 0.4374 (ptp-170) REVERT: R 398 ASP cc_start: 0.5050 (t0) cc_final: 0.4800 (m-30) REVERT: A 347 ARG cc_start: 0.6949 (ptp90) cc_final: 0.5927 (ttt90) REVERT: A 420 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6510 (t80) REVERT: A 439 ASP cc_start: 0.6978 (m-30) cc_final: 0.6356 (p0) REVERT: A 491 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6708 (mm-30) REVERT: A 509 GLU cc_start: 0.7610 (tp30) cc_final: 0.7335 (tt0) REVERT: A 693 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: A 785 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8047 (mm-40) REVERT: A 937 ASN cc_start: 0.6825 (m110) cc_final: 0.6278 (m110) REVERT: A 953 GLU cc_start: 0.8003 (pt0) cc_final: 0.7523 (tp30) REVERT: A 1012 LYS cc_start: 0.3209 (OUTLIER) cc_final: 0.1816 (ptmt) REVERT: A 1601 GLN cc_start: 0.7801 (mp10) cc_final: 0.7330 (mt0) REVERT: A 1645 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7608 (mtpt) REVERT: B 43 GLN cc_start: 0.7911 (tp40) cc_final: 0.7286 (tt0) REVERT: B 201 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7409 (mttt) REVERT: B 229 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.5495 (t80) REVERT: B 261 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.7984 (ttp-170) REVERT: B 335 ARG cc_start: 0.6982 (ttt90) cc_final: 0.6556 (ttp-110) REVERT: B 441 LYS cc_start: 0.7506 (mtmm) cc_final: 0.7177 (mttm) REVERT: B 550 ARG cc_start: 0.7582 (mmt-90) cc_final: 0.6949 (ptt90) REVERT: B 588 ILE cc_start: 0.8612 (pt) cc_final: 0.8336 (pt) REVERT: B 641 TYR cc_start: 0.8385 (m-10) cc_final: 0.7779 (m-80) REVERT: B 690 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: B 726 MET cc_start: 0.7786 (ptp) cc_final: 0.7545 (ptp) REVERT: B 924 LYS cc_start: 0.8546 (ptmt) cc_final: 0.8203 (mmtt) REVERT: B 940 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5521 (tp30) REVERT: B 943 ILE cc_start: 0.8436 (mt) cc_final: 0.7992 (tp) REVERT: B 960 ILE cc_start: 0.8895 (mm) cc_final: 0.8605 (mm) REVERT: B 970 LYS cc_start: 0.5703 (pttt) cc_final: 0.5158 (mmtt) REVERT: B 1057 MET cc_start: 0.8379 (mmm) cc_final: 0.8056 (ttm) REVERT: B 1151 ILE cc_start: 0.5069 (OUTLIER) cc_final: 0.4779 (pp) REVERT: B 1188 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6534 (mm-30) REVERT: C 278 GLU cc_start: 0.6755 (tp30) cc_final: 0.6365 (tp30) REVERT: E 11 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6919 (tpp-160) REVERT: E 30 ILE cc_start: 0.8007 (mm) cc_final: 0.7607 (mm) REVERT: E 96 PHE cc_start: 0.6836 (t80) cc_final: 0.6118 (t80) REVERT: G 21 LYS cc_start: 0.7386 (mttt) cc_final: 0.6977 (tmmt) REVERT: G 85 GLU cc_start: 0.6982 (tt0) cc_final: 0.6425 (pp20) REVERT: G 110 ASP cc_start: 0.6969 (m-30) cc_final: 0.6765 (t0) REVERT: G 128 GLN cc_start: 0.8119 (mp10) cc_final: 0.7865 (mp10) REVERT: G 134 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5139 (tm-30) REVERT: H 9 ILE cc_start: 0.8712 (mt) cc_final: 0.8492 (mm) REVERT: H 145 ARG cc_start: 0.6929 (ttp-110) cc_final: 0.6371 (ttm-80) REVERT: I 41 GLN cc_start: 0.6088 (tp-100) cc_final: 0.5845 (tt0) REVERT: J 2 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6763 (pp) REVERT: J 68 LYS cc_start: 0.7408 (tttp) cc_final: 0.5902 (mmtm) REVERT: K 85 ASP cc_start: 0.7878 (t0) cc_final: 0.7579 (t0) REVERT: L 42 ARG cc_start: 0.5958 (ptt-90) cc_final: 0.5623 (mmt-90) REVERT: N 80 MET cc_start: 0.4131 (ttp) cc_final: 0.3019 (tmm) REVERT: N 107 MET cc_start: 0.4862 (mmm) cc_final: 0.3272 (mmm) REVERT: N 166 LEU cc_start: 0.0920 (OUTLIER) cc_final: 0.0542 (pp) REVERT: O 149 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6852 (tttt) REVERT: O 179 PHE cc_start: 0.5284 (m-10) cc_final: 0.4812 (m-10) REVERT: O 182 MET cc_start: 0.6007 (tpt) cc_final: 0.5628 (tpt) REVERT: O 369 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7908 (tmmt) REVERT: O 382 GLN cc_start: 0.7130 (pm20) cc_final: 0.6309 (mp10) REVERT: O 451 ASN cc_start: 0.5201 (m-40) cc_final: 0.4853 (p0) REVERT: O 452 ARG cc_start: 0.5437 (tpm170) cc_final: 0.5228 (tpm170) REVERT: O 467 MET cc_start: 0.6541 (mmm) cc_final: 0.5841 (mmt) REVERT: O 486 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4003 (m-10) REVERT: O 541 PHE cc_start: 0.5842 (t80) cc_final: 0.5568 (t80) REVERT: O 612 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6045 (tp30) outliers start: 133 outliers final: 93 residues processed: 718 average time/residue: 0.6977 time to fit residues: 856.0902 Evaluate side-chains 708 residues out of total 5543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 600 time to evaluate : 5.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 108 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 388 ASN Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 287 ASN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 940 GLU Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain O residue 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 362 optimal weight: 2.9990 chunk 583 optimal weight: 3.9990 chunk 355 optimal weight: 0.0980 chunk 276 optimal weight: 9.9990 chunk 405 optimal weight: 3.9990 chunk 611 optimal weight: 4.9990 chunk 563 optimal weight: 0.3980 chunk 487 optimal weight: 0.0970 chunk 50 optimal weight: 6.9990 chunk 376 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: