Starting phenix.real_space_refine on Sun Feb 25 10:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/02_2024/6rqh_4982.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/02_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_4982/02_2024/6rqh_4982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/02_2024/6rqh_4982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/02_2024/6rqh_4982.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqh_4982/02_2024/6rqh_4982.pdb" } 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 Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q GLU 241": "OE1" <-> "OE2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "N PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 26.69, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.22 Conformation dependent library (CDL) restraints added in 8.5 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: 15.44 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: 14.86 Time building geometry restraints manager: 20.84 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: 97.41 - 104.78: 1187 104.78 - 112.14: 24768 112.14 - 119.51: 19101 119.51 - 126.87: 24807 126.87 - 134.24: 793 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 2.440 nonbonded pdb=" OD1 ASN A 840 " pdb=" OG1 THR A 844 " model vdw 2.232 2.440 nonbonded pdb=" O ALA A 951 " pdb=" OG1 THR I 98 " model vdw 2.237 2.440 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 14.330 Check model and map are aligned: 0.840 Set scattering table: 0.520 Process input model: 133.370 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.190 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 32 poor density : 1374 time to evaluate : 5.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7272 time to fit residues: 1634.9398 Evaluate side-chains 769 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 762 time to evaluate : 5.564 ------------------------------------------------------------------------------- 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: 0.7980 chunk 465 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 481 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 292 optimal weight: 0.4980 chunk 358 optimal weight: 0.3980 chunk 557 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 228 ASN Q 351 ASN Q 511 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 ASN S 461 HIS ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 483 HIS ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 554 ASN S 613 HIS S 665 ASN S 758 ASN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN R 179 HIS ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN R 434 GLN M 71 GLN M 89 GLN A 60 ASN A 179 ASN A 264 ASN A 332 GLN A 431 GLN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 560 GLN A 592 GLN A 706 HIS A 748 ASN A 753 ASN A 785 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A 926 GLN A 937 ASN A1047 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1314 GLN A1319 ASN A1447 GLN A1487 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 433 ASN B 462 GLN ** 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 745 GLN B 923 GLN B1066 HIS C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS E 61 GLN G 26 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 66 ASN O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 549 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52042 Z= 0.191 Angle : 0.664 10.595 70656 Z= 0.352 Chirality : 0.045 0.281 7887 Planarity : 0.005 0.070 8789 Dihedral : 13.861 175.026 7528 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.60 % Favored : 92.38 % Rotamer: Outliers : 2.74 % Allowed : 10.93 % Favored : 86.34 % 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: -4.28 (0.09), residues: 6049 helix: -3.12 (0.08), residues: 2010 sheet: -2.81 (0.18), residues: 683 loop : -2.70 (0.10), residues: 3356 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 0.027 0.002 PHE E 135 TYR 0.028 0.002 TYR R 410 ARG 0.011 0.001 ARG B 909 *********************** 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 1012 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 862 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 21 ARG cc_start: 0.1206 (pmt-80) cc_final: 0.0488 (tpp80) REVERT: Q 287 TRP cc_start: 0.1379 (t60) cc_final: 0.0872 (t60) REVERT: Q 292 GLU cc_start: 0.1853 (pm20) cc_final: 0.1317 (mp0) REVERT: Q 301 HIS cc_start: 0.4006 (m90) cc_final: 0.3237 (t-90) REVERT: S 33 THR cc_start: 0.1942 (t) cc_final: 0.1602 (m) REVERT: S 221 ARG cc_start: 0.4819 (ttt90) cc_final: 0.3619 (ttp80) REVERT: S 256 ARG cc_start: 0.2523 (ptm-80) cc_final: 0.2092 (ptp-170) REVERT: S 369 PHE cc_start: 0.3864 (t80) cc_final: 0.2644 (m-10) REVERT: S 386 MET cc_start: 0.3633 (tpp) cc_final: 0.3283 (tpp) REVERT: S 471 MET cc_start: 0.0636 (tmm) cc_final: -0.0451 (ppp) REVERT: S 484 ARG cc_start: 0.6796 (mmm-85) cc_final: 0.5799 (mtt180) REVERT: S 667 ASP cc_start: -0.0796 (t0) cc_final: -0.1083 (t0) REVERT: S 691 VAL cc_start: 0.3028 (p) cc_final: 0.2510 (t) REVERT: S 693 PHE cc_start: 0.0943 (m-80) cc_final: -0.0642 (p90) REVERT: S 772 ILE cc_start: 0.3934 (mm) cc_final: 0.3614 (pt) REVERT: S 777 MET cc_start: 0.2524 (ttp) cc_final: 0.2074 (tpt) REVERT: R 23 TYR cc_start: 0.1005 (t80) cc_final: 0.0737 (t80) REVERT: R 291 ARG cc_start: 0.4142 (mpt180) cc_final: 0.2020 (tpt-90) REVERT: R 307 LYS cc_start: 0.3170 (mmmt) cc_final: 0.2705 (tttm) REVERT: M 42 LYS cc_start: 0.5166 (pptt) cc_final: 0.4620 (mttp) REVERT: A 22 LYS cc_start: 0.7012 (mmmm) cc_final: 0.5856 (mttt) REVERT: A 209 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7907 (p) REVERT: A 347 ARG cc_start: 0.6906 (ptp90) cc_final: 0.5939 (ttt90) REVERT: A 420 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 491 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6080 (mm-30) REVERT: A 509 GLU cc_start: 0.7462 (tp30) cc_final: 0.7179 (tp30) REVERT: A 633 MET cc_start: 0.7998 (mtt) cc_final: 0.7744 (ttm) REVERT: A 693 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: A 785 GLN cc_start: 0.8446 (mm110) cc_final: 0.8090 (mm110) REVERT: A 930 LEU cc_start: 0.8020 (mt) cc_final: 0.7495 (mt) REVERT: A 960 MET cc_start: 0.7892 (mtt) cc_final: 0.7663 (mtp) REVERT: A 1020 GLN cc_start: 0.7786 (tt0) cc_final: 0.7559 (tp40) REVERT: A 1028 GLU cc_start: 0.7725 (tp30) cc_final: 0.7054 (tp30) REVERT: A 1092 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7019 (tm-30) REVERT: A 1245 ASP cc_start: 0.6398 (p0) cc_final: 0.5879 (m-30) REVERT: A 1246 VAL cc_start: 0.7947 (p) cc_final: 0.7491 (t) REVERT: A 1444 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7135 (mtt90) REVERT: A 1469 TRP cc_start: 0.8086 (p-90) cc_final: 0.7693 (p-90) REVERT: A 1471 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5362 (mt-10) REVERT: A 1533 GLU cc_start: 0.6445 (pm20) cc_final: 0.6012 (pm20) REVERT: A 1535 PHE cc_start: 0.6635 (m-80) cc_final: 0.6335 (m-80) REVERT: A 1600 ARG cc_start: 0.7452 (mtm180) cc_final: 0.6631 (mtp85) REVERT: A 1601 GLN cc_start: 0.7840 (mt0) cc_final: 0.7603 (mp10) REVERT: A 1632 GLU cc_start: 0.7558 (tp30) cc_final: 0.7349 (tp30) REVERT: B 43 GLN cc_start: 0.7883 (tp40) cc_final: 0.7189 (tt0) REVERT: B 229 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.5617 (t80) REVERT: B 261 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7928 (ttp-170) REVERT: B 348 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: B 441 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7341 (mttp) REVERT: B 444 ARG cc_start: 0.8200 (ptp90) cc_final: 0.7866 (tpt170) REVERT: B 461 MET cc_start: 0.7291 (mmm) cc_final: 0.6195 (mmt) REVERT: B 489 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6882 (mt-10) REVERT: B 495 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7810 (tpt170) REVERT: B 550 ARG cc_start: 0.7381 (mmt-90) cc_final: 0.6969 (ptt90) REVERT: B 554 GLN cc_start: 0.7688 (pm20) cc_final: 0.7402 (mt0) REVERT: B 588 ILE cc_start: 0.8506 (pt) cc_final: 0.8300 (pt) REVERT: B 591 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8242 (tttp) REVERT: B 740 LYS cc_start: 0.8281 (ptpp) cc_final: 0.8048 (mttt) REVERT: B 970 LYS cc_start: 0.6368 (ttpt) cc_final: 0.6064 (ptmt) REVERT: B 1043 LYS cc_start: 0.4541 (mmmt) cc_final: 0.4249 (tppt) REVERT: B 1049 THR cc_start: 0.8238 (t) cc_final: 0.7962 (m) REVERT: B 1057 MET cc_start: 0.8293 (mmm) cc_final: 0.7923 (ttm) REVERT: B 1134 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6311 (mtt-85) REVERT: B 1151 ILE cc_start: 0.4718 (OUTLIER) cc_final: 0.4202 (pp) REVERT: B 1157 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6416 (mm-40) REVERT: B 1188 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 1199 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7402 (t0) REVERT: C 278 GLU cc_start: 0.6741 (tp30) cc_final: 0.6500 (tp30) REVERT: C 319 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6676 (mtt90) REVERT: C 327 TYR cc_start: 0.7742 (t80) cc_final: 0.7514 (t80) REVERT: E 93 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6541 (tpp) REVERT: F 144 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7397 (mt-10) REVERT: G 21 LYS cc_start: 0.7378 (mttt) cc_final: 0.6733 (tmmt) REVERT: G 85 GLU cc_start: 0.6678 (tt0) cc_final: 0.6154 (pp20) REVERT: G 88 LYS cc_start: 0.8229 (ttpp) cc_final: 0.8017 (mttt) REVERT: G 102 GLU cc_start: 0.7699 (pp20) cc_final: 0.7371 (tm-30) REVERT: H 145 ARG cc_start: 0.7103 (ttp-110) cc_final: 0.6576 (ttm-80) REVERT: I 97 HIS cc_start: 0.0630 (t-90) cc_final: 0.0354 (t-90) REVERT: J 68 LYS cc_start: 0.6753 (tttp) cc_final: 0.5849 (mmtm) REVERT: L 42 ARG cc_start: 0.6271 (ptt-90) cc_final: 0.5713 (mmt-90) REVERT: N 80 MET cc_start: 0.3638 (ttp) cc_final: 0.3188 (tmm) REVERT: O 137 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7348 (mp) REVERT: O 151 TRP cc_start: 0.6943 (t-100) cc_final: 0.6483 (t-100) REVERT: O 229 ILE cc_start: 0.8032 (mp) cc_final: 0.7635 (mm) REVERT: O 369 LYS cc_start: 0.8234 (ptpt) cc_final: 0.7569 (tmmt) REVERT: O 382 GLN cc_start: 0.6829 (pm20) cc_final: 0.6335 (mp10) REVERT: O 486 PHE cc_start: 0.4834 (m-10) cc_final: 0.4273 (m-10) REVERT: O 541 PHE cc_start: 0.5567 (t80) cc_final: 0.5325 (t80) REVERT: O 583 GLN cc_start: 0.6845 (tp40) cc_final: 0.6614 (pm20) outliers start: 150 outliers final: 80 residues processed: 964 average time/residue: 0.6563 time to fit residues: 1039.3506 Evaluate side-chains 753 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 663 time to evaluate : 5.627 ------------------------------------------------------------------------------- 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 43 LEU 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 489 PHE Chi-restraints excluded: chain S residue 544 SER 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 210 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 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 500 VAL Chi-restraints excluded: chain A residue 563 THR 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 871 ASP 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 348 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 779 THR 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 B residue 1199 ASN 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 D residue 18 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET 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 116 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 167 THR 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 94 ASP 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 325 ILE 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: 0.5980 chunk 379 optimal weight: 3.9990 chunk 153 optimal weight: 0.0020 chunk 558 optimal weight: 0.4980 chunk 603 optimal weight: 4.9990 chunk 497 optimal weight: 0.1980 chunk 553 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 448 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 294 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 ASN R 207 ASN R 212 HIS ** R 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** 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 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 153 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** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3158 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= 0.156 Angle : 0.585 10.799 70656 Z= 0.307 Chirality : 0.043 0.222 7887 Planarity : 0.004 0.059 8789 Dihedral : 13.524 174.490 7523 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.03 % Favored : 92.96 % Rotamer: Outliers : 2.99 % Allowed : 12.33 % Favored : 84.68 % 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: -3.67 (0.09), residues: 6049 helix: -2.41 (0.10), residues: 2021 sheet: -2.51 (0.19), residues: 641 loop : -2.46 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 125 HIS 0.007 0.001 HIS S 461 PHE 0.039 0.001 PHE B 577 TYR 0.025 0.001 TYR O 602 ARG 0.009 0.000 ARG B 909 *********************** 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 917 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 753 time to evaluate : 6.747 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: 0.0461 (pmt-80) cc_final: 0.0160 (tpp80) REVERT: Q 164 ILE cc_start: 0.2055 (OUTLIER) cc_final: 0.1803 (tt) REVERT: Q 287 TRP cc_start: 0.1247 (t60) cc_final: 0.0700 (t60) REVERT: Q 292 GLU cc_start: 0.2474 (pm20) cc_final: 0.1889 (mp0) REVERT: Q 301 HIS cc_start: 0.4036 (m90) cc_final: 0.3246 (t-90) REVERT: S 62 LYS cc_start: 0.3445 (tmtm) cc_final: 0.2820 (mmmt) REVERT: S 221 ARG cc_start: 0.5090 (ttt90) cc_final: 0.3308 (ptt180) REVERT: S 386 MET cc_start: 0.3706 (tpp) cc_final: 0.3319 (tpp) REVERT: S 399 TRP cc_start: 0.1452 (m-90) cc_final: -0.2241 (m100) REVERT: S 471 MET cc_start: 0.0634 (tmm) cc_final: -0.0527 (ppp) REVERT: S 484 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.5837 (mtt180) REVERT: S 667 ASP cc_start: -0.1212 (t0) cc_final: -0.1438 (t0) REVERT: S 693 PHE cc_start: 0.0724 (m-80) cc_final: -0.0723 (p90) REVERT: S 772 ILE cc_start: 0.4100 (mm) cc_final: 0.3837 (pt) REVERT: S 777 MET cc_start: 0.2505 (ttp) cc_final: 0.2049 (tpt) REVERT: R 23 TYR cc_start: 0.0890 (t80) cc_final: 0.0652 (t80) REVERT: R 236 PHE cc_start: 0.3806 (t80) cc_final: 0.3535 (t80) REVERT: R 291 ARG cc_start: 0.4033 (mpt180) cc_final: 0.1997 (tpt-90) REVERT: R 307 LYS cc_start: 0.3390 (mmmt) cc_final: 0.3006 (tttm) REVERT: M 42 LYS cc_start: 0.5114 (pptt) cc_final: 0.4494 (mttp) REVERT: A 22 LYS cc_start: 0.7015 (mmmm) cc_final: 0.6065 (ttpt) REVERT: A 129 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6938 (pp) REVERT: A 347 ARG cc_start: 0.6953 (ptp90) cc_final: 0.5949 (ttt90) REVERT: A 420 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6718 (t80) REVERT: A 424 MET cc_start: 0.6752 (mmp) cc_final: 0.5829 (ptm) REVERT: A 491 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6685 (mm-30) REVERT: A 509 GLU cc_start: 0.7448 (tp30) cc_final: 0.7085 (tp30) REVERT: A 601 MET cc_start: 0.8324 (ptp) cc_final: 0.8082 (mtm) REVERT: A 632 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 785 GLN cc_start: 0.8410 (mm110) cc_final: 0.8000 (mm110) REVERT: A 1028 GLU cc_start: 0.7583 (tp30) cc_final: 0.7046 (tp30) REVERT: A 1092 GLU cc_start: 0.7784 (mm-30) cc_final: 0.6933 (tm-30) REVERT: A 1245 ASP cc_start: 0.6368 (p0) cc_final: 0.5819 (m-30) REVERT: A 1246 VAL cc_start: 0.7927 (p) cc_final: 0.7388 (t) REVERT: A 1315 ASN cc_start: 0.8061 (t0) cc_final: 0.7535 (t0) REVERT: A 1444 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7334 (mtt90) REVERT: A 1469 TRP cc_start: 0.8047 (p-90) cc_final: 0.7436 (p-90) REVERT: A 1471 GLU cc_start: 0.5262 (mt-10) cc_final: 0.5036 (mt-10) REVERT: A 1533 GLU cc_start: 0.6479 (pm20) cc_final: 0.5947 (tm-30) REVERT: A 1535 PHE cc_start: 0.6561 (m-80) cc_final: 0.6262 (m-80) REVERT: A 1601 GLN cc_start: 0.7812 (mt0) cc_final: 0.7608 (mp10) REVERT: B 43 GLN cc_start: 0.7829 (tp40) cc_final: 0.7206 (tt0) REVERT: B 229 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.5615 (t80) REVERT: B 348 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: B 441 LYS cc_start: 0.7597 (mtmm) cc_final: 0.7304 (mttp) REVERT: B 444 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7846 (tpt170) REVERT: B 461 MET cc_start: 0.7383 (mmm) cc_final: 0.6131 (mmt) REVERT: B 489 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6957 (mt-10) REVERT: B 495 ARG cc_start: 0.8033 (tpt90) cc_final: 0.7781 (tpt170) REVERT: B 519 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6787 (mmtm) REVERT: B 550 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7057 (ptt90) REVERT: B 588 ILE cc_start: 0.8625 (pt) cc_final: 0.8380 (pt) REVERT: B 591 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8196 (tttp) REVERT: B 740 LYS cc_start: 0.8258 (ptpp) cc_final: 0.8044 (mttt) REVERT: B 1049 THR cc_start: 0.8081 (t) cc_final: 0.7861 (m) REVERT: B 1057 MET cc_start: 0.8349 (mmm) cc_final: 0.7955 (ttm) REVERT: B 1134 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6408 (mtt90) REVERT: B 1151 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4361 (pp) REVERT: B 1157 GLN cc_start: 0.6673 (mm-40) cc_final: 0.6293 (mm-40) REVERT: B 1188 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6740 (mm-30) REVERT: B 1199 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7404 (t0) REVERT: C 41 GLU cc_start: 0.7057 (mp0) cc_final: 0.6628 (mp0) REVERT: C 278 GLU cc_start: 0.6792 (tp30) cc_final: 0.6504 (tp30) REVERT: E 96 PHE cc_start: 0.6873 (t80) cc_final: 0.6627 (t80) REVERT: E 122 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7180 (mttm) REVERT: F 56 GLU cc_start: 0.5286 (OUTLIER) cc_final: 0.4692 (mt-10) REVERT: F 85 MET cc_start: 0.8352 (ttm) cc_final: 0.7987 (mtt) REVERT: F 144 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7400 (mt-10) REVERT: F 153 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7991 (t) REVERT: G 21 LYS cc_start: 0.7497 (mttt) cc_final: 0.6795 (tmmt) REVERT: H 145 ARG cc_start: 0.7172 (ttp-110) cc_final: 0.6626 (ttm-80) REVERT: I 7 LEU cc_start: 0.6323 (mp) cc_final: 0.5638 (tp) REVERT: J 68 LYS cc_start: 0.6720 (tttp) cc_final: 0.5910 (mmtm) REVERT: K 81 MET cc_start: 0.8395 (mmm) cc_final: 0.8148 (mmm) REVERT: L 42 ARG cc_start: 0.6147 (ptt-90) cc_final: 0.5668 (mmt-90) REVERT: N 36 LYS cc_start: 0.2714 (mmtt) cc_final: 0.1463 (ptpp) REVERT: N 80 MET cc_start: 0.3653 (ttp) cc_final: 0.3021 (tmm) REVERT: N 166 LEU cc_start: 0.0949 (OUTLIER) cc_final: -0.0025 (pp) REVERT: N 178 GLU cc_start: 0.2569 (mp0) cc_final: 0.1348 (pm20) REVERT: O 149 LYS cc_start: 0.7432 (ttpt) cc_final: 0.7029 (tttt) REVERT: O 151 TRP cc_start: 0.6710 (t-100) cc_final: 0.6338 (t-100) REVERT: O 182 MET cc_start: 0.6422 (ttt) cc_final: 0.6170 (ttt) REVERT: O 369 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7735 (tmmt) REVERT: O 382 GLN cc_start: 0.6829 (pm20) cc_final: 0.6365 (mp10) REVERT: O 467 MET cc_start: 0.6284 (mmm) cc_final: 0.5603 (mmt) REVERT: O 541 PHE cc_start: 0.5749 (t80) cc_final: 0.5457 (t80) REVERT: O 583 GLN cc_start: 0.6875 (tp40) cc_final: 0.6648 (pm20) REVERT: O 602 TYR cc_start: 0.5461 (t80) cc_final: 0.5173 (t80) outliers start: 164 outliers final: 80 residues processed: 865 average time/residue: 0.6686 time to fit residues: 961.7689 Evaluate side-chains 737 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 645 time to evaluate : 5.745 ------------------------------------------------------------------------------- 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 362 THR Chi-restraints excluded: chain S residue 210 THR 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 S residue 544 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 286 GLN Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain A residue 129 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 707 THR Chi-restraints excluded: chain A residue 871 ASP 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 1316 VAL Chi-restraints excluded: chain A residue 1333 ILE 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 281 CYS Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 358 VAL 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 585 CYS 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 1088 LEU 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 1199 ASN Chi-restraints excluded: chain C residue 92 ILE 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 313 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 56 GLU 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 116 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP 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 20 SER 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 N residue 166 LEU 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 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: 3.9990 chunk 419 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 266 optimal weight: 0.1980 chunk 375 optimal weight: 1.9990 chunk 560 optimal weight: 7.9990 chunk 593 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 531 optimal weight: 0.7980 chunk 159 optimal weight: 0.0030 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 479 HIS ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 ASN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1026 GLN A1568 ASN B 45 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 423 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 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** I 97 HIS N 61 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 52042 Z= 0.174 Angle : 0.572 11.233 70656 Z= 0.299 Chirality : 0.043 0.289 7887 Planarity : 0.004 0.056 8789 Dihedral : 13.410 175.843 7523 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 3.12 % Allowed : 13.46 % Favored : 83.42 % 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: -3.28 (0.10), residues: 6049 helix: -2.00 (0.10), residues: 2023 sheet: -2.40 (0.19), residues: 636 loop : -2.26 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 316 HIS 0.009 0.001 HIS B 547 PHE 0.019 0.001 PHE S 578 TYR 0.020 0.001 TYR B 317 ARG 0.006 0.000 ARG R 283 *********************** 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 840 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 669 time to evaluate : 5.442 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: Q 21 ARG cc_start: 0.0612 (pmt-80) cc_final: 0.0218 (tpp80) REVERT: Q 287 TRP cc_start: 0.1267 (t60) cc_final: 0.0720 (t60) REVERT: Q 292 GLU cc_start: 0.2128 (pm20) cc_final: 0.1543 (mp0) REVERT: Q 301 HIS cc_start: 0.4107 (m90) cc_final: 0.3294 (t-90) REVERT: S 35 LYS cc_start: 0.1589 (tttt) cc_final: 0.1135 (ttpt) REVERT: S 62 LYS cc_start: 0.3582 (tmtm) cc_final: 0.2895 (mmmt) REVERT: S 221 ARG cc_start: 0.5124 (ttt90) cc_final: 0.3432 (ptt180) REVERT: S 386 MET cc_start: 0.3698 (tpp) cc_final: 0.3271 (tpp) REVERT: S 399 TRP cc_start: 0.1347 (m-90) cc_final: -0.2407 (m100) REVERT: S 471 MET cc_start: 0.0568 (tmm) cc_final: -0.0295 (tmm) REVERT: S 484 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.5868 (mtt180) REVERT: S 693 PHE cc_start: 0.0664 (m-80) cc_final: -0.0776 (p90) REVERT: S 777 MET cc_start: 0.2517 (ttp) cc_final: 0.2047 (tpt) REVERT: R 236 PHE cc_start: 0.3890 (t80) cc_final: 0.3595 (t80) REVERT: R 291 ARG cc_start: 0.3746 (mpt180) cc_final: 0.1747 (tmt-80) REVERT: R 302 ARG cc_start: 0.4015 (mtt-85) cc_final: 0.3787 (ptp-170) REVERT: R 307 LYS cc_start: 0.3380 (mmmt) cc_final: 0.2981 (tttm) REVERT: R 314 TRP cc_start: 0.4804 (m100) cc_final: 0.3926 (m100) REVERT: R 359 MET cc_start: 0.5014 (mmm) cc_final: 0.4751 (mmm) REVERT: A 129 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7015 (pp) REVERT: A 347 ARG cc_start: 0.6943 (ptp90) cc_final: 0.5875 (ttt90) REVERT: A 420 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 424 MET cc_start: 0.6886 (mmp) cc_final: 0.5835 (ptm) REVERT: A 509 GLU cc_start: 0.7433 (tp30) cc_final: 0.7202 (tt0) REVERT: A 601 MET cc_start: 0.8391 (ptp) cc_final: 0.8135 (mtm) REVERT: A 635 MET cc_start: 0.7468 (tmm) cc_final: 0.7158 (tmm) REVERT: A 693 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: A 785 GLN cc_start: 0.8432 (mm110) cc_final: 0.7999 (mm110) REVERT: A 1028 GLU cc_start: 0.7551 (tp30) cc_final: 0.7148 (tp30) REVERT: A 1092 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6909 (tm-30) REVERT: A 1245 ASP cc_start: 0.6286 (p0) cc_final: 0.5460 (m-30) REVERT: A 1246 VAL cc_start: 0.7847 (p) cc_final: 0.7396 (p) REVERT: A 1315 ASN cc_start: 0.7968 (t0) cc_final: 0.7533 (t0) REVERT: A 1469 TRP cc_start: 0.8119 (p-90) cc_final: 0.7588 (p-90) REVERT: A 1471 GLU cc_start: 0.5318 (mt-10) cc_final: 0.4919 (mt-10) REVERT: A 1533 GLU cc_start: 0.6506 (pm20) cc_final: 0.5990 (tm-30) REVERT: A 1535 PHE cc_start: 0.6566 (m-80) cc_final: 0.6212 (m-10) REVERT: A 1645 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7571 (mtpt) REVERT: B 43 GLN cc_start: 0.7881 (tp40) cc_final: 0.7275 (tt0) REVERT: B 229 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.5338 (t80) REVERT: B 275 MET cc_start: 0.7365 (ttm) cc_final: 0.6980 (ttm) REVERT: B 441 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7378 (mttp) REVERT: B 444 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7904 (tpt170) REVERT: B 461 MET cc_start: 0.7457 (mmm) cc_final: 0.6230 (mmt) REVERT: B 489 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6931 (mt-10) REVERT: B 495 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7803 (tpt170) REVERT: B 550 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.6988 (ptt90) REVERT: B 588 ILE cc_start: 0.8622 (pt) cc_final: 0.8394 (pt) REVERT: B 943 ILE cc_start: 0.8301 (mt) cc_final: 0.7726 (tp) REVERT: B 977 ILE cc_start: 0.1426 (OUTLIER) cc_final: 0.1211 (mt) REVERT: B 1049 THR cc_start: 0.8049 (t) cc_final: 0.7846 (m) REVERT: B 1057 MET cc_start: 0.8386 (mmm) cc_final: 0.8007 (ttm) REVERT: B 1134 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6485 (mtt90) REVERT: B 1151 ILE cc_start: 0.4828 (OUTLIER) cc_final: 0.4462 (pp) REVERT: B 1157 GLN cc_start: 0.6728 (mm-40) cc_final: 0.6342 (mm-40) REVERT: B 1188 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6658 (mm-30) REVERT: C 278 GLU cc_start: 0.6827 (tp30) cc_final: 0.6459 (tp30) REVERT: E 96 PHE cc_start: 0.6938 (t80) cc_final: 0.6215 (t80) REVERT: F 56 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.4777 (mt-10) REVERT: F 85 MET cc_start: 0.8372 (ttm) cc_final: 0.8000 (mtt) REVERT: F 111 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7744 (pp) REVERT: F 144 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7378 (mt-10) REVERT: F 153 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8111 (t) REVERT: G 21 LYS cc_start: 0.7486 (mttt) cc_final: 0.6829 (tmmt) REVERT: G 85 GLU cc_start: 0.6848 (tt0) cc_final: 0.6348 (pp20) REVERT: G 134 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5430 (tm-30) REVERT: H 145 ARG cc_start: 0.7077 (ttp-110) cc_final: 0.6585 (ttm-80) REVERT: I 7 LEU cc_start: 0.6291 (mp) cc_final: 0.5508 (tp) REVERT: J 68 LYS cc_start: 0.7017 (tttp) cc_final: 0.5928 (mmtp) REVERT: K 85 ASP cc_start: 0.8139 (t0) cc_final: 0.7359 (t0) REVERT: L 42 ARG cc_start: 0.6248 (ptt-90) cc_final: 0.5728 (mmt-90) REVERT: N 80 MET cc_start: 0.3734 (ttp) cc_final: 0.3067 (tmm) REVERT: N 166 LEU cc_start: 0.1387 (OUTLIER) cc_final: 0.0411 (pp) REVERT: N 178 GLU cc_start: 0.2772 (mp0) cc_final: 0.1538 (pm20) REVERT: O 149 LYS cc_start: 0.7363 (ttpt) cc_final: 0.6988 (tttt) REVERT: O 151 TRP cc_start: 0.6980 (t-100) cc_final: 0.6380 (t-100) REVERT: O 369 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7741 (tmmt) REVERT: O 382 GLN cc_start: 0.6962 (pm20) cc_final: 0.6440 (mp10) REVERT: O 451 ASN cc_start: 0.5646 (m-40) cc_final: 0.4549 (p0) REVERT: O 452 ARG cc_start: 0.5406 (tpm170) cc_final: 0.5199 (tpm170) REVERT: O 467 MET cc_start: 0.6443 (mmm) cc_final: 0.5661 (mmt) REVERT: O 541 PHE cc_start: 0.5794 (t80) cc_final: 0.5467 (t80) REVERT: O 583 GLN cc_start: 0.6828 (tp40) cc_final: 0.6611 (pm20) REVERT: O 602 TYR cc_start: 0.5572 (t80) cc_final: 0.5361 (t80) outliers start: 171 outliers final: 113 residues processed: 788 average time/residue: 0.6111 time to fit residues: 804.5469 Evaluate side-chains 744 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 619 time to evaluate : 6.080 ------------------------------------------------------------------------------- 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 Q residue 375 LEU 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 303 VAL 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 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 279 SER Chi-restraints excluded: chain R residue 286 GLN 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 209 THR Chi-restraints excluded: chain A residue 236 CYS 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 440 SER 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 904 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1012 LYS 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 1333 ILE 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 281 CYS 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 358 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 476 LEU 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 726 MET Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 779 THR 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 1088 LEU 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 B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 116 VAL 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 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 138 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 124 VAL Chi-restraints excluded: chain G residue 134 GLU 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 7 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP 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 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 N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 325 ILE Chi-restraints excluded: chain O residue 348 THR 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 509 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 494 optimal weight: 0.7980 chunk 336 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 441 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 506 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 303 optimal weight: 0.0970 chunk 532 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 ASN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 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 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 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 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 52042 Z= 0.179 Angle : 0.570 12.772 70656 Z= 0.296 Chirality : 0.043 0.222 7887 Planarity : 0.004 0.053 8789 Dihedral : 13.362 178.758 7523 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.24 % Favored : 92.74 % Rotamer: Outliers : 3.54 % Allowed : 14.16 % Favored : 82.31 % 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: -3.03 (0.10), residues: 6049 helix: -1.71 (0.11), residues: 2046 sheet: -2.29 (0.19), residues: 663 loop : -2.15 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 316 HIS 0.010 0.001 HIS B 547 PHE 0.018 0.001 PHE A1472 TYR 0.037 0.001 TYR B 317 ARG 0.004 0.000 ARG A 855 *********************** 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 864 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 670 time to evaluate : 5.714 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: 0.0649 (OUTLIER) cc_final: 0.0178 (tpp80) REVERT: Q 287 TRP cc_start: 0.1253 (t60) cc_final: 0.0748 (t60) REVERT: Q 292 GLU cc_start: 0.2186 (pm20) cc_final: 0.1571 (mp0) REVERT: Q 301 HIS cc_start: 0.4053 (m90) cc_final: 0.3233 (t-90) REVERT: S 35 LYS cc_start: 0.1777 (tttt) cc_final: 0.1519 (ttpt) REVERT: S 221 ARG cc_start: 0.5155 (ttt90) cc_final: 0.3489 (ptt180) REVERT: S 386 MET cc_start: 0.3609 (tpp) cc_final: 0.3105 (mpp) REVERT: S 471 MET cc_start: 0.0445 (tmm) cc_final: -0.0467 (tmm) REVERT: S 484 ARG cc_start: 0.6832 (mmm-85) cc_final: 0.5774 (mtt180) REVERT: S 693 PHE cc_start: 0.0582 (m-80) cc_final: -0.0808 (p90) REVERT: S 777 MET cc_start: 0.2625 (ttp) cc_final: 0.2145 (tpt) REVERT: R 236 PHE cc_start: 0.3899 (t80) cc_final: 0.3561 (t80) REVERT: R 291 ARG cc_start: 0.3720 (mpt180) cc_final: 0.1759 (tmt-80) REVERT: R 307 LYS cc_start: 0.3375 (mmmt) cc_final: 0.2967 (tttm) REVERT: R 349 ILE cc_start: 0.6768 (tt) cc_final: 0.6304 (mt) REVERT: A 129 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (pp) REVERT: A 236 CYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5139 (p) REVERT: A 347 ARG cc_start: 0.6911 (ptp90) cc_final: 0.5853 (ttt90) REVERT: A 420 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6691 (t80) REVERT: A 424 MET cc_start: 0.6817 (mmp) cc_final: 0.5681 (ptm) REVERT: A 509 GLU cc_start: 0.7512 (tp30) cc_final: 0.7269 (tt0) REVERT: A 693 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: A 785 GLN cc_start: 0.8452 (mm110) cc_final: 0.7990 (mm110) REVERT: A 1012 LYS cc_start: 0.3197 (OUTLIER) cc_final: 0.1769 (ptmt) REVERT: A 1092 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6886 (tm-30) REVERT: A 1315 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (t0) REVERT: A 1469 TRP cc_start: 0.8113 (p-90) cc_final: 0.7555 (p-90) REVERT: A 1471 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5225 (mt-10) REVERT: A 1535 PHE cc_start: 0.6600 (m-80) cc_final: 0.6213 (m-10) REVERT: A 1601 GLN cc_start: 0.8005 (mp10) cc_final: 0.7639 (mt0) REVERT: B 229 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.5316 (t80) REVERT: B 275 MET cc_start: 0.7409 (ttm) cc_final: 0.7181 (tpp) REVERT: B 441 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7382 (mttp) REVERT: B 461 MET cc_start: 0.7531 (mmm) cc_final: 0.6262 (mmt) REVERT: B 489 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6940 (mt-10) REVERT: B 588 ILE cc_start: 0.8717 (pt) cc_final: 0.8492 (pt) REVERT: B 943 ILE cc_start: 0.8224 (mt) cc_final: 0.7798 (tp) REVERT: B 977 ILE cc_start: 0.1515 (OUTLIER) cc_final: 0.1308 (mt) REVERT: B 1057 MET cc_start: 0.8376 (mmm) cc_final: 0.8016 (ttm) REVERT: B 1134 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6500 (mtt90) REVERT: B 1151 ILE cc_start: 0.5162 (OUTLIER) cc_final: 0.4880 (pp) REVERT: B 1157 GLN cc_start: 0.6572 (mm-40) cc_final: 0.6207 (mm-40) REVERT: B 1188 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6587 (mm-30) REVERT: C 278 GLU cc_start: 0.6850 (tp30) cc_final: 0.6416 (tp30) REVERT: D 26 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: E 96 PHE cc_start: 0.6939 (t80) cc_final: 0.6206 (t80) REVERT: F 56 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.4857 (mt-10) REVERT: F 111 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7803 (pp) REVERT: F 144 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7333 (mt-10) REVERT: G 21 LYS cc_start: 0.7543 (mttt) cc_final: 0.6932 (tmmt) REVERT: G 85 GLU cc_start: 0.6826 (tt0) cc_final: 0.6341 (pp20) REVERT: G 87 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8534 (tt) REVERT: G 110 ASP cc_start: 0.6977 (m-30) cc_final: 0.6635 (t0) REVERT: G 123 TYR cc_start: 0.8454 (m-80) cc_final: 0.7995 (m-10) REVERT: G 134 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5353 (tm-30) REVERT: G 138 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.3195 (t80) REVERT: H 9 ILE cc_start: 0.8698 (mt) cc_final: 0.8479 (mm) REVERT: H 145 ARG cc_start: 0.7099 (ttp-110) cc_final: 0.6537 (ttm-80) REVERT: I 7 LEU cc_start: 0.6379 (mp) cc_final: 0.5494 (tp) REVERT: J 2 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7007 (pp) REVERT: J 68 LYS cc_start: 0.7080 (tttp) cc_final: 0.5986 (mmtm) REVERT: K 85 ASP cc_start: 0.8077 (t0) cc_final: 0.7516 (t0) REVERT: L 42 ARG cc_start: 0.6230 (ptt-90) cc_final: 0.5688 (mmt-90) REVERT: N 80 MET cc_start: 0.3655 (ttp) cc_final: 0.2732 (tmm) REVERT: N 107 MET cc_start: 0.5127 (mmm) cc_final: 0.3455 (mmm) REVERT: N 166 LEU cc_start: 0.1269 (OUTLIER) cc_final: 0.0435 (pp) REVERT: N 178 GLU cc_start: 0.2708 (mp0) cc_final: 0.1403 (pm20) REVERT: O 149 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6928 (tttt) REVERT: O 151 TRP cc_start: 0.6977 (t-100) cc_final: 0.6348 (t-100) REVERT: O 369 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7785 (tmmt) REVERT: O 382 GLN cc_start: 0.7086 (pm20) cc_final: 0.6289 (mp10) REVERT: O 451 ASN cc_start: 0.5864 (m-40) cc_final: 0.4816 (p0) REVERT: O 452 ARG cc_start: 0.5456 (tpm170) cc_final: 0.5218 (tpm170) REVERT: O 467 MET cc_start: 0.6664 (mmm) cc_final: 0.6033 (mmt) REVERT: O 541 PHE cc_start: 0.5807 (t80) cc_final: 0.5486 (t80) REVERT: O 551 ARG cc_start: 0.4776 (mmt180) cc_final: 0.4485 (ptt-90) REVERT: O 602 TYR cc_start: 0.5767 (t80) cc_final: 0.5544 (t80) outliers start: 194 outliers final: 128 residues processed: 803 average time/residue: 0.6205 time to fit residues: 836.6959 Evaluate side-chains 770 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 624 time to evaluate : 5.646 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 285 MET Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 318 ILE 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 489 PHE Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 286 GLN 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 236 CYS 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 400 ASN 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 440 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 519 LEU 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 739 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1225 ILE 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 B residue 95 LEU 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 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS 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 358 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 476 LEU 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 726 MET Chi-restraints excluded: chain B residue 779 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 1038 HIS Chi-restraints excluded: chain B residue 1088 LEU 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 B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN 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 18 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 LEU 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 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 167 THR Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP 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 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 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 243 GLU 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 509 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 199 optimal weight: 0.7980 chunk 534 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 348 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 594 optimal weight: 0.0770 chunk 493 optimal weight: 0.7980 chunk 275 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 311 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 ASN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN B 282 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** 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** H 134 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52042 Z= 0.142 Angle : 0.542 11.807 70656 Z= 0.280 Chirality : 0.042 0.214 7887 Planarity : 0.004 0.056 8789 Dihedral : 13.269 179.823 7523 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.73 % Favored : 93.26 % Rotamer: Outliers : 3.16 % Allowed : 14.98 % Favored : 81.87 % 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: -2.72 (0.10), residues: 6049 helix: -1.35 (0.11), residues: 2034 sheet: -2.13 (0.19), residues: 653 loop : -2.04 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 314 HIS 0.007 0.001 HIS S 461 PHE 0.018 0.001 PHE A 437 TYR 0.032 0.001 TYR B 317 ARG 0.011 0.000 ARG H 130 *********************** 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 843 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 670 time to evaluate : 6.518 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: 0.0770 (OUTLIER) cc_final: 0.0240 (tpp80) REVERT: Q 287 TRP cc_start: 0.0936 (t60) cc_final: 0.0544 (t60) REVERT: Q 292 GLU cc_start: 0.2445 (pm20) cc_final: 0.1856 (mp0) REVERT: Q 301 HIS cc_start: 0.4105 (m90) cc_final: 0.3297 (t-90) REVERT: S 221 ARG cc_start: 0.5235 (ttt90) cc_final: 0.3519 (ptt180) REVERT: S 362 ARG cc_start: 0.1329 (tpt90) cc_final: 0.0943 (mmm-85) REVERT: S 386 MET cc_start: 0.3613 (tpp) cc_final: 0.3106 (mpp) REVERT: S 484 ARG cc_start: 0.6835 (mmm-85) cc_final: 0.5775 (mtt180) REVERT: S 693 PHE cc_start: 0.0560 (m-80) cc_final: -0.0853 (p90) REVERT: S 777 MET cc_start: 0.2621 (ttp) cc_final: 0.2069 (tpt) REVERT: R 290 TYR cc_start: 0.3875 (m-80) cc_final: 0.3330 (m-80) REVERT: R 291 ARG cc_start: 0.3468 (mpt180) cc_final: 0.1595 (tmt-80) REVERT: R 307 LYS cc_start: 0.3316 (mmmt) cc_final: 0.2961 (tttt) REVERT: R 349 ILE cc_start: 0.6784 (tt) cc_final: 0.6333 (mt) REVERT: M 42 LYS cc_start: 0.5212 (pptt) cc_final: 0.4499 (mttp) REVERT: A 129 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6998 (pp) REVERT: A 236 CYS cc_start: 0.5327 (OUTLIER) cc_final: 0.5065 (p) REVERT: A 347 ARG cc_start: 0.6881 (ptp90) cc_final: 0.5847 (ttt90) REVERT: A 420 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6541 (t80) REVERT: A 693 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: A 785 GLN cc_start: 0.8417 (mm110) cc_final: 0.7917 (mm110) REVERT: A 928 MET cc_start: 0.8449 (ptm) cc_final: 0.8007 (ptp) REVERT: A 937 ASN cc_start: 0.6935 (m110) cc_final: 0.6399 (m110) REVERT: A 1012 LYS cc_start: 0.3275 (OUTLIER) cc_final: 0.1955 (ptmt) REVERT: A 1092 GLU cc_start: 0.7749 (mm-30) cc_final: 0.6856 (tm-30) REVERT: A 1315 ASN cc_start: 0.7966 (t0) cc_final: 0.7736 (t0) REVERT: A 1469 TRP cc_start: 0.7990 (p-90) cc_final: 0.7597 (p-90) REVERT: A 1535 PHE cc_start: 0.6618 (m-80) cc_final: 0.6350 (m-80) REVERT: A 1601 GLN cc_start: 0.7977 (mp10) cc_final: 0.7566 (mt0) REVERT: A 1627 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7700 (mt) REVERT: B 43 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7218 (tt0) REVERT: B 229 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.5091 (t80) REVERT: B 231 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6538 (m90) REVERT: B 441 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7347 (mttm) REVERT: B 489 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6900 (mt-10) REVERT: B 588 ILE cc_start: 0.8689 (pt) cc_final: 0.8465 (pt) REVERT: B 606 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.5867 (t0) REVERT: B 839 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7596 (mtmm) REVERT: B 861 TYR cc_start: 0.7701 (p90) cc_final: 0.7209 (p90) REVERT: B 943 ILE cc_start: 0.8297 (mt) cc_final: 0.7817 (tp) REVERT: B 1057 MET cc_start: 0.8428 (mmm) cc_final: 0.8042 (ttm) REVERT: B 1151 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4869 (pp) REVERT: B 1157 GLN cc_start: 0.6518 (mm-40) cc_final: 0.6205 (mm-40) REVERT: B 1188 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6442 (mm-30) REVERT: C 278 GLU cc_start: 0.6765 (tp30) cc_final: 0.6337 (tp30) REVERT: E 30 ILE cc_start: 0.8003 (mm) cc_final: 0.7797 (mm) REVERT: E 93 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6463 (tpp) REVERT: E 96 PHE cc_start: 0.6918 (t80) cc_final: 0.6227 (t80) REVERT: F 111 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7913 (pp) REVERT: G 21 LYS cc_start: 0.7450 (mttt) cc_final: 0.6921 (tmmt) REVERT: G 85 GLU cc_start: 0.6784 (tt0) cc_final: 0.6330 (pp20) REVERT: G 87 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (tt) REVERT: G 110 ASP cc_start: 0.7129 (m-30) cc_final: 0.6820 (t0) REVERT: G 128 GLN cc_start: 0.7966 (mp10) cc_final: 0.7193 (mp10) REVERT: G 134 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5442 (tm-30) REVERT: H 145 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6567 (ttm-80) REVERT: I 7 LEU cc_start: 0.6455 (mp) cc_final: 0.5532 (tp) REVERT: J 2 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6952 (pp) REVERT: J 68 LYS cc_start: 0.7243 (tttp) cc_final: 0.5870 (mmtp) REVERT: K 85 ASP cc_start: 0.7961 (t0) cc_final: 0.7370 (t0) REVERT: L 42 ARG cc_start: 0.6112 (ptt-90) cc_final: 0.5638 (mmt-90) REVERT: N 80 MET cc_start: 0.3781 (ttp) cc_final: 0.2887 (tmm) REVERT: N 107 MET cc_start: 0.4888 (mmm) cc_final: 0.3577 (mmm) REVERT: N 178 GLU cc_start: 0.2621 (mp0) cc_final: 0.1302 (pm20) REVERT: O 149 LYS cc_start: 0.7247 (ttpt) cc_final: 0.6916 (tttt) REVERT: O 151 TRP cc_start: 0.7051 (t-100) cc_final: 0.6386 (t-100) REVERT: O 182 MET cc_start: 0.6338 (tpt) cc_final: 0.6093 (tpt) REVERT: O 369 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7808 (tmmt) REVERT: O 382 GLN cc_start: 0.7063 (pm20) cc_final: 0.6297 (mp10) REVERT: O 451 ASN cc_start: 0.5634 (m-40) cc_final: 0.4820 (p0) REVERT: O 452 ARG cc_start: 0.5428 (tpm170) cc_final: 0.5221 (tpm170) REVERT: O 467 MET cc_start: 0.6513 (mmm) cc_final: 0.5891 (mmt) REVERT: O 504 LYS cc_start: 0.5541 (mtmt) cc_final: 0.4622 (pptt) REVERT: O 541 PHE cc_start: 0.5842 (t80) cc_final: 0.5529 (t80) outliers start: 173 outliers final: 102 residues processed: 789 average time/residue: 0.6260 time to fit residues: 832.1299 Evaluate side-chains 727 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 609 time to evaluate : 5.208 ------------------------------------------------------------------------------- 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 235 SER 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 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 286 GLN 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 209 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 310 THR 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 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 793 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1627 LEU 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 255 ASP Chi-restraints excluded: chain B residue 281 CYS 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 358 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1088 LEU 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 1151 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN 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 201 GLU 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 40 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 159 ASP 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 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 237 HIS Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 4 VAL 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 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 73 ILE Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 360 VAL Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 434 LEU 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: 3.9990 chunk 66 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 433 optimal weight: 3.9990 chunk 336 optimal weight: 0.8980 chunk 500 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 591 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 360 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 ASN ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52042 Z= 0.200 Angle : 0.581 11.103 70656 Z= 0.298 Chirality : 0.043 0.211 7887 Planarity : 0.004 0.050 8789 Dihedral : 13.235 175.771 7521 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.65 % Favored : 92.33 % Rotamer: Outliers : 3.23 % Allowed : 15.27 % Favored : 81.50 % 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: -2.62 (0.10), residues: 6049 helix: -1.22 (0.11), residues: 2038 sheet: -2.19 (0.19), residues: 652 loop : -1.99 (0.10), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 316 HIS 0.007 0.001 HIS S 461 PHE 0.021 0.001 PHE H 6 TYR 0.017 0.001 TYR B1014 ARG 0.007 0.000 ARG B 225 *********************** 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 804 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 627 time to evaluate : 5.504 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: Q 21 ARG cc_start: 0.0908 (OUTLIER) cc_final: 0.0362 (tpp80) REVERT: Q 108 PHE cc_start: 0.0266 (OUTLIER) cc_final: -0.0170 (t80) REVERT: Q 287 TRP cc_start: 0.0960 (t60) cc_final: 0.0622 (t60) REVERT: Q 292 GLU cc_start: 0.2267 (pm20) cc_final: 0.1668 (mp0) REVERT: Q 301 HIS cc_start: 0.4136 (m90) cc_final: 0.3325 (t-90) REVERT: S 221 ARG cc_start: 0.5256 (ttt90) cc_final: 0.3521 (ptt180) REVERT: S 362 ARG cc_start: 0.1337 (tpt90) cc_final: 0.0990 (mmm-85) REVERT: S 386 MET cc_start: 0.3521 (tpp) cc_final: 0.3185 (tpp) REVERT: S 471 MET cc_start: -0.0133 (tpp) cc_final: -0.1274 (tmm) REVERT: S 484 ARG cc_start: 0.6840 (mmm-85) cc_final: 0.5770 (mtt180) REVERT: S 693 PHE cc_start: 0.0559 (m-80) cc_final: -0.0918 (p90) REVERT: S 777 MET cc_start: 0.2368 (ttp) cc_final: 0.1855 (tpt) REVERT: R 291 ARG cc_start: 0.3482 (mpt180) cc_final: 0.1490 (tmt-80) REVERT: R 307 LYS cc_start: 0.3222 (mmmt) cc_final: 0.2901 (tttm) REVERT: R 349 ILE cc_start: 0.6824 (tt) cc_final: 0.6373 (mt) REVERT: M 103 LYS cc_start: 0.5424 (mtpp) cc_final: 0.5221 (mmmt) REVERT: A 49 LEU cc_start: 0.7016 (mp) cc_final: 0.6705 (mt) REVERT: A 129 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7060 (pp) REVERT: A 238 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5875 (ppp) REVERT: A 347 ARG cc_start: 0.6942 (ptp90) cc_final: 0.5951 (ttt90) REVERT: A 420 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 424 MET cc_start: 0.6623 (mmp) cc_final: 0.5538 (ptm) REVERT: A 439 ASP cc_start: 0.7183 (m-30) cc_final: 0.6385 (p0) REVERT: A 693 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: A 785 GLN cc_start: 0.8485 (mm110) cc_final: 0.7972 (mm110) REVERT: A 1012 LYS cc_start: 0.3158 (OUTLIER) cc_final: 0.1715 (ptmt) REVERT: A 1092 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6879 (tm-30) REVERT: A 1315 ASN cc_start: 0.7958 (t0) cc_final: 0.7731 (t0) REVERT: A 1469 TRP cc_start: 0.7884 (p-90) cc_final: 0.7615 (p-90) REVERT: A 1535 PHE cc_start: 0.6641 (m-80) cc_final: 0.6399 (m-80) REVERT: A 1601 GLN cc_start: 0.7932 (mp10) cc_final: 0.7553 (mt0) REVERT: B 43 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7302 (tt0) REVERT: B 229 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.4976 (t80) REVERT: B 268 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6607 (mm-30) REVERT: B 441 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7245 (mttm) REVERT: B 489 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6909 (mt-10) REVERT: B 588 ILE cc_start: 0.8729 (pt) cc_final: 0.8506 (pt) REVERT: B 606 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.5991 (t0) REVERT: B 861 TYR cc_start: 0.7736 (p90) cc_final: 0.7337 (p90) REVERT: B 924 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8277 (mmtt) REVERT: B 940 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5409 (tp30) REVERT: B 943 ILE cc_start: 0.8293 (mt) cc_final: 0.7799 (tp) REVERT: B 1057 MET cc_start: 0.8445 (mmm) cc_final: 0.8027 (ttm) REVERT: B 1151 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4905 (pp) REVERT: B 1157 GLN cc_start: 0.6622 (mm-40) cc_final: 0.6247 (mm-40) REVERT: B 1188 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6500 (mm-30) REVERT: C 278 GLU cc_start: 0.6845 (tp30) cc_final: 0.6330 (tp30) REVERT: D 26 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: E 30 ILE cc_start: 0.8023 (mm) cc_final: 0.7816 (mm) REVERT: E 96 PHE cc_start: 0.6888 (t80) cc_final: 0.6176 (t80) REVERT: F 111 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7925 (pp) REVERT: G 21 LYS cc_start: 0.7457 (mttt) cc_final: 0.6916 (tmmt) REVERT: G 85 GLU cc_start: 0.6938 (tt0) cc_final: 0.6444 (pp20) REVERT: G 110 ASP cc_start: 0.7135 (m-30) cc_final: 0.6773 (t0) REVERT: G 126 GLN cc_start: 0.8123 (pt0) cc_final: 0.7432 (pt0) REVERT: G 128 GLN cc_start: 0.8158 (mp10) cc_final: 0.7235 (mp10) REVERT: G 134 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5320 (tm-30) REVERT: H 9 ILE cc_start: 0.8729 (mt) cc_final: 0.8505 (mm) REVERT: H 145 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6571 (ttm-80) REVERT: J 2 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7063 (pp) REVERT: J 68 LYS cc_start: 0.7493 (tttp) cc_final: 0.5922 (mmtm) REVERT: K 85 ASP cc_start: 0.8091 (t0) cc_final: 0.7456 (t0) REVERT: L 42 ARG cc_start: 0.6200 (ptt-90) cc_final: 0.5748 (mmt-90) REVERT: N 80 MET cc_start: 0.3920 (ttp) cc_final: 0.3080 (tmm) REVERT: N 107 MET cc_start: 0.4987 (mmm) cc_final: 0.3803 (mmm) REVERT: N 166 LEU cc_start: 0.1261 (OUTLIER) cc_final: 0.0614 (pp) REVERT: O 149 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6941 (tttt) REVERT: O 369 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7764 (tmmt) REVERT: O 382 GLN cc_start: 0.7190 (pm20) cc_final: 0.6553 (mp10) REVERT: O 451 ASN cc_start: 0.5571 (m-40) cc_final: 0.4728 (p0) REVERT: O 467 MET cc_start: 0.6629 (mmm) cc_final: 0.5885 (mmt) REVERT: O 541 PHE cc_start: 0.5955 (t80) cc_final: 0.5611 (t80) outliers start: 177 outliers final: 128 residues processed: 743 average time/residue: 0.6236 time to fit residues: 780.6936 Evaluate side-chains 742 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 598 time to evaluate : 5.379 ------------------------------------------------------------------------------- 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 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 203 ILE 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 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 489 PHE Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 286 GLN Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR 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 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 357 MET Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 400 ASN 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 440 SER Chi-restraints excluded: chain A residue 519 LEU 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 793 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1308 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 1563 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR 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 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 302 LEU 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 358 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 726 MET 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 900 THR Chi-restraints excluded: chain B residue 940 GLU 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 1151 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN 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 201 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 MET 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 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 111 THR Chi-restraints excluded: chain G residue 116 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 H residue 7 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP 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 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain N residue 154 ARG 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 360 VAL Chi-restraints excluded: chain O residue 434 LEU 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: 0.0570 chunk 236 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 178 optimal weight: 0.0570 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 376 optimal weight: 1.9990 chunk 403 optimal weight: 0.0030 chunk 292 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 465 optimal weight: 5.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- 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** ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1314 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4375 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= 0.140 Angle : 0.545 11.755 70656 Z= 0.279 Chirality : 0.041 0.186 7887 Planarity : 0.004 0.053 8789 Dihedral : 13.104 175.217 7520 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.65 % Rotamer: Outliers : 2.61 % Allowed : 16.25 % Favored : 81.14 % 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: -2.34 (0.10), residues: 6049 helix: -0.96 (0.11), residues: 2049 sheet: -1.95 (0.20), residues: 651 loop : -1.87 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 316 HIS 0.007 0.001 HIS S 461 PHE 0.022 0.001 PHE C 179 TYR 0.033 0.001 TYR B 778 ARG 0.009 0.000 ARG R 283 *********************** 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 787 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 644 time to evaluate : 5.453 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: 0.0859 (OUTLIER) cc_final: 0.0358 (tpp80) REVERT: Q 108 PHE cc_start: 0.0294 (OUTLIER) cc_final: -0.0218 (t80) REVERT: Q 287 TRP cc_start: 0.0877 (t60) cc_final: 0.0515 (t60) REVERT: Q 292 GLU cc_start: 0.2430 (pm20) cc_final: 0.1863 (mp0) REVERT: Q 301 HIS cc_start: 0.4093 (m90) cc_final: 0.3296 (t-90) REVERT: S 386 MET cc_start: 0.3543 (tpp) cc_final: 0.3213 (tpp) REVERT: S 471 MET cc_start: -0.0447 (tpp) cc_final: -0.1521 (tmm) REVERT: S 484 ARG cc_start: 0.6624 (mmm-85) cc_final: 0.5635 (mtt180) REVERT: S 693 PHE cc_start: 0.0424 (m-80) cc_final: -0.0954 (p90) REVERT: S 777 MET cc_start: 0.2789 (ttp) cc_final: 0.2136 (tpt) REVERT: R 290 TYR cc_start: 0.3793 (m-80) cc_final: 0.3240 (m-80) REVERT: R 291 ARG cc_start: 0.3477 (mpt180) cc_final: 0.1496 (tmt-80) REVERT: R 302 ARG cc_start: 0.4083 (mtt90) cc_final: 0.3053 (ptm-80) REVERT: R 307 LYS cc_start: 0.3166 (mmmt) cc_final: 0.2855 (tttm) REVERT: R 349 ILE cc_start: 0.6814 (tt) cc_final: 0.6378 (mt) REVERT: A 49 LEU cc_start: 0.6862 (mp) cc_final: 0.6561 (mt) REVERT: A 129 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6941 (pp) REVERT: A 238 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.6029 (pmm) REVERT: A 347 ARG cc_start: 0.6898 (ptp90) cc_final: 0.5926 (ttt90) REVERT: A 420 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6470 (t80) REVERT: A 424 MET cc_start: 0.6502 (mmp) cc_final: 0.5562 (ptm) REVERT: A 439 ASP cc_start: 0.7041 (m-30) cc_final: 0.6339 (p0) REVERT: A 693 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: A 785 GLN cc_start: 0.8388 (mm110) cc_final: 0.7870 (mm110) REVERT: A 937 ASN cc_start: 0.6937 (m110) cc_final: 0.6446 (m110) REVERT: A 1012 LYS cc_start: 0.3333 (OUTLIER) cc_final: 0.2007 (ptmt) REVERT: A 1020 GLN cc_start: 0.7662 (tp40) cc_final: 0.7394 (tp40) REVERT: A 1092 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6907 (tm-30) REVERT: A 1126 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6871 (tptt) REVERT: A 1249 GLU cc_start: 0.6728 (tt0) cc_final: 0.6243 (mp0) REVERT: A 1471 GLU cc_start: 0.5850 (tt0) cc_final: 0.5225 (mt-10) REVERT: B 43 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7149 (tt0) REVERT: B 229 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.5347 (t80) REVERT: B 268 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6653 (mm-30) REVERT: B 441 LYS cc_start: 0.7542 (mtmm) cc_final: 0.7231 (mttm) REVERT: B 489 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6858 (mt-10) REVERT: B 588 ILE cc_start: 0.8716 (pt) cc_final: 0.8482 (pt) REVERT: B 606 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.5878 (t0) REVERT: B 861 TYR cc_start: 0.7764 (p90) cc_final: 0.7368 (p90) REVERT: B 924 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8218 (mmtt) REVERT: B 941 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6556 (t) REVERT: B 943 ILE cc_start: 0.8338 (mt) cc_final: 0.7958 (tp) REVERT: B 1057 MET cc_start: 0.8477 (mmm) cc_final: 0.8049 (ttm) REVERT: B 1151 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4962 (pp) REVERT: B 1157 GLN cc_start: 0.6659 (mm-40) cc_final: 0.6319 (mm-40) REVERT: B 1188 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6412 (mm-30) REVERT: C 278 GLU cc_start: 0.6759 (tp30) cc_final: 0.6313 (tp30) REVERT: D 26 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: E 30 ILE cc_start: 0.7999 (mm) cc_final: 0.7765 (mm) REVERT: E 93 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6515 (tpp) REVERT: E 96 PHE cc_start: 0.6848 (t80) cc_final: 0.6145 (t80) REVERT: F 111 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7967 (pp) REVERT: G 21 LYS cc_start: 0.7415 (mttt) cc_final: 0.6910 (tmmt) REVERT: G 85 GLU cc_start: 0.7004 (tt0) cc_final: 0.6505 (pp20) REVERT: G 102 GLU cc_start: 0.7531 (pp20) cc_final: 0.7238 (pp20) REVERT: G 110 ASP cc_start: 0.7051 (m-30) cc_final: 0.6800 (t0) REVERT: G 126 GLN cc_start: 0.8305 (pt0) cc_final: 0.7940 (pt0) REVERT: G 128 GLN cc_start: 0.8009 (mp10) cc_final: 0.7101 (mp10) REVERT: H 9 ILE cc_start: 0.8715 (mt) cc_final: 0.8502 (mm) REVERT: H 128 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6696 (m-40) REVERT: H 145 ARG cc_start: 0.7117 (ttp-110) cc_final: 0.6610 (ttm-80) REVERT: J 2 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6901 (pp) REVERT: J 68 LYS cc_start: 0.7377 (tttp) cc_final: 0.5903 (mmtm) REVERT: K 85 ASP cc_start: 0.7975 (t0) cc_final: 0.7484 (t0) REVERT: K 91 TYR cc_start: 0.8279 (p90) cc_final: 0.7974 (p90) REVERT: L 42 ARG cc_start: 0.6098 (ptt-90) cc_final: 0.5741 (mmt-90) REVERT: N 80 MET cc_start: 0.3942 (ttp) cc_final: 0.3081 (tmm) REVERT: N 107 MET cc_start: 0.4992 (mmm) cc_final: 0.3862 (mmm) REVERT: N 166 LEU cc_start: 0.1177 (OUTLIER) cc_final: 0.0649 (pp) REVERT: O 149 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6896 (tttt) REVERT: O 369 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7907 (tmmt) REVERT: O 382 GLN cc_start: 0.7164 (pm20) cc_final: 0.6361 (mp10) REVERT: O 451 ASN cc_start: 0.5358 (m-40) cc_final: 0.4702 (p0) REVERT: O 467 MET cc_start: 0.6562 (mmm) cc_final: 0.5816 (mmt) REVERT: O 541 PHE cc_start: 0.5896 (t80) cc_final: 0.5577 (t80) REVERT: O 551 ARG cc_start: 0.5268 (mmt180) cc_final: 0.4873 (ptt90) REVERT: O 612 GLU cc_start: 0.6375 (mm-30) cc_final: 0.6037 (tp30) outliers start: 143 outliers final: 97 residues processed: 737 average time/residue: 0.6186 time to fit residues: 770.9646 Evaluate side-chains 702 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 587 time to evaluate : 5.574 ------------------------------------------------------------------------------- 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 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 203 ILE 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 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR 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 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 360 LEU 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 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 793 ILE Chi-restraints excluded: chain A residue 938 VAL 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 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 B residue 95 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS 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 358 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 941 THR 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 B residue 1199 ASN 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 201 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 111 LEU 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 138 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 4 VAL 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 K residue 140 LYS Chi-restraints excluded: chain N residue 154 ARG 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 509 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 538 optimal weight: 4.9990 chunk 566 optimal weight: 0.6980 chunk 517 optimal weight: 1.9990 chunk 551 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 433 optimal weight: 0.8980 chunk 169 optimal weight: 0.0670 chunk 498 optimal weight: 5.9990 chunk 521 optimal weight: 0.9990 chunk 549 optimal weight: 2.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1314 GLN ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 480 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 52042 Z= 0.177 Angle : 0.568 11.468 70656 Z= 0.290 Chirality : 0.042 0.240 7887 Planarity : 0.004 0.053 8789 Dihedral : 13.081 172.254 7520 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.53 % Rotamer: Outliers : 2.77 % Allowed : 16.33 % Favored : 80.90 % 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: -2.28 (0.11), residues: 6049 helix: -0.86 (0.11), residues: 2048 sheet: -2.05 (0.19), residues: 675 loop : -1.83 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 316 HIS 0.007 0.001 HIS S 461 PHE 0.027 0.001 PHE B 376 TYR 0.015 0.001 TYR B1014 ARG 0.007 0.000 ARG R 283 *********************** 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 758 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 606 time to evaluate : 5.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 21 ARG cc_start: 0.0915 (OUTLIER) cc_final: 0.0316 (tpp80) REVERT: Q 108 PHE cc_start: 0.0267 (OUTLIER) cc_final: -0.0244 (t80) REVERT: Q 287 TRP cc_start: 0.0896 (t60) cc_final: 0.0544 (t60) REVERT: Q 292 GLU cc_start: 0.2633 (pm20) cc_final: 0.2107 (mp0) REVERT: Q 301 HIS cc_start: 0.4149 (m90) cc_final: 0.3290 (t-90) REVERT: S 35 LYS cc_start: 0.1824 (tttt) cc_final: 0.1229 (ttpt) REVERT: S 386 MET cc_start: 0.3627 (tpp) cc_final: 0.3291 (tpp) REVERT: S 484 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.6325 (mmm-85) REVERT: S 693 PHE cc_start: 0.0430 (m-80) cc_final: -0.0953 (p90) REVERT: S 777 MET cc_start: 0.2403 (ttp) cc_final: 0.1860 (tpt) REVERT: R 236 PHE cc_start: 0.3272 (t80) cc_final: 0.2591 (t80) REVERT: R 291 ARG cc_start: 0.3467 (mpt180) cc_final: 0.1491 (tmt-80) REVERT: R 307 LYS cc_start: 0.3135 (mmmt) cc_final: 0.2825 (tttm) REVERT: R 349 ILE cc_start: 0.6878 (tt) cc_final: 0.6436 (mt) REVERT: M 103 LYS cc_start: 0.5404 (mtpp) cc_final: 0.5187 (mmmt) REVERT: A 49 LEU cc_start: 0.6963 (mp) cc_final: 0.6666 (mt) REVERT: A 129 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6951 (pp) REVERT: A 238 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5081 (ppp) REVERT: A 347 ARG cc_start: 0.6975 (ptp90) cc_final: 0.5948 (ttt90) REVERT: A 420 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6469 (t80) REVERT: A 424 MET cc_start: 0.6619 (mmp) cc_final: 0.5660 (ptm) REVERT: A 439 ASP cc_start: 0.7171 (m-30) cc_final: 0.6413 (p0) REVERT: A 555 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8154 (ttmt) REVERT: A 693 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: A 785 GLN cc_start: 0.8438 (mm110) cc_final: 0.7918 (mm110) REVERT: A 937 ASN cc_start: 0.7103 (m110) cc_final: 0.6603 (m110) REVERT: A 1012 LYS cc_start: 0.3440 (OUTLIER) cc_final: 0.2091 (ptmt) REVERT: A 1020 GLN cc_start: 0.7696 (tp40) cc_final: 0.7474 (tp40) REVERT: A 1092 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6983 (tm-30) REVERT: A 1126 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6908 (tptt) REVERT: A 1469 TRP cc_start: 0.7832 (p-90) cc_final: 0.7594 (p-90) REVERT: B 43 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7079 (tt0) REVERT: B 229 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.5365 (t80) REVERT: B 268 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6645 (mm-30) REVERT: B 441 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7207 (mttm) REVERT: B 489 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6867 (mt-10) REVERT: B 606 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.5950 (t0) REVERT: B 924 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8229 (mmtt) REVERT: B 940 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.5231 (tp30) REVERT: B 941 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6569 (t) REVERT: B 943 ILE cc_start: 0.8321 (mt) cc_final: 0.7912 (tp) REVERT: B 1057 MET cc_start: 0.8495 (mmm) cc_final: 0.7998 (ttm) REVERT: B 1151 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4833 (pp) REVERT: B 1157 GLN cc_start: 0.6668 (mm-40) cc_final: 0.6403 (mm-40) REVERT: B 1188 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6541 (mm-30) REVERT: C 278 GLU cc_start: 0.6831 (tp30) cc_final: 0.6343 (tp30) REVERT: D 26 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: E 30 ILE cc_start: 0.8026 (mm) cc_final: 0.7660 (mm) REVERT: E 93 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6448 (tpp) REVERT: E 96 PHE cc_start: 0.6848 (t80) cc_final: 0.6139 (t80) REVERT: G 21 LYS cc_start: 0.7404 (mttt) cc_final: 0.6962 (tmmt) REVERT: G 85 GLU cc_start: 0.7085 (tt0) cc_final: 0.6609 (pp20) REVERT: G 102 GLU cc_start: 0.7709 (pp20) cc_final: 0.7211 (pp20) REVERT: G 110 ASP cc_start: 0.7066 (m-30) cc_final: 0.6827 (t0) REVERT: G 134 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5319 (tm-30) REVERT: H 9 ILE cc_start: 0.8720 (mt) cc_final: 0.8508 (mm) REVERT: H 145 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6566 (ttm-80) REVERT: J 2 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6997 (pp) REVERT: J 68 LYS cc_start: 0.7539 (tttp) cc_final: 0.5932 (mmtm) REVERT: K 85 ASP cc_start: 0.8042 (t0) cc_final: 0.7460 (t0) REVERT: L 42 ARG cc_start: 0.6138 (ptt-90) cc_final: 0.5770 (mmt-90) REVERT: N 80 MET cc_start: 0.3931 (ttp) cc_final: 0.3194 (tmm) REVERT: N 107 MET cc_start: 0.5043 (mmm) cc_final: 0.3906 (mmm) REVERT: N 166 LEU cc_start: 0.1061 (OUTLIER) cc_final: 0.0616 (pp) REVERT: O 149 LYS cc_start: 0.7244 (ttpt) cc_final: 0.6880 (tttt) REVERT: O 369 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7815 (tmmt) REVERT: O 382 GLN cc_start: 0.7234 (pm20) cc_final: 0.6584 (mp10) REVERT: O 451 ASN cc_start: 0.5531 (m-40) cc_final: 0.4843 (p0) REVERT: O 452 ARG cc_start: 0.5381 (tpt90) cc_final: 0.5095 (tpt90) REVERT: O 467 MET cc_start: 0.6577 (mmm) cc_final: 0.5864 (mmt) REVERT: O 541 PHE cc_start: 0.5918 (t80) cc_final: 0.5588 (t80) REVERT: O 551 ARG cc_start: 0.5967 (mmt180) cc_final: 0.5534 (ptt90) outliers start: 152 outliers final: 113 residues processed: 705 average time/residue: 0.6232 time to fit residues: 741.2872 Evaluate side-chains 709 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 577 time to evaluate : 5.460 ------------------------------------------------------------------------------- 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 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 203 ILE 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 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 638 LEU Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR 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 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 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 400 ASN 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 440 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 555 LYS 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 793 ILE Chi-restraints excluded: chain A residue 938 VAL 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 1333 ILE 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 B residue 95 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS 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 446 MET Chi-restraints excluded: chain B residue 480 GLN 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 606 ASP Chi-restraints excluded: chain B residue 726 MET 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 940 GLU Chi-restraints excluded: chain B residue 941 THR 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 B residue 1199 ASN 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 201 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 159 ASP 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 134 GLU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP 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 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 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 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 362 optimal weight: 0.5980 chunk 583 optimal weight: 6.9990 chunk 355 optimal weight: 0.0980 chunk 276 optimal weight: 5.9990 chunk 405 optimal weight: 6.9990 chunk 611 optimal weight: 3.9990 chunk 563 optimal weight: 6.9990 chunk 487 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 376 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1314 GLN ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 52042 Z= 0.192 Angle : 0.648 59.199 70656 Z= 0.344 Chirality : 0.043 0.469 7887 Planarity : 0.004 0.087 8789 Dihedral : 13.085 172.224 7520 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.47 % Favored : 92.51 % Rotamer: Outliers : 2.63 % Allowed : 16.84 % Favored : 80.54 % 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: -2.26 (0.11), residues: 6049 helix: -0.83 (0.11), residues: 2048 sheet: -2.04 (0.19), residues: 675 loop : -1.82 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 316 HIS 0.010 0.001 HIS Q 171 PHE 0.025 0.001 PHE B 376 TYR 0.016 0.001 TYR B1014 ARG 0.021 0.000 ARG H 130 ********************** REFINEMENT MACRO_CYCLE 10 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 720 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 576 time to evaluate : 5.994 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: Q 21 ARG cc_start: 0.0905 (OUTLIER) cc_final: 0.0320 (tpp80) REVERT: Q 108 PHE cc_start: 0.0275 (OUTLIER) cc_final: -0.0243 (t80) REVERT: Q 287 TRP cc_start: 0.0893 (t60) cc_final: 0.0541 (t60) REVERT: Q 292 GLU cc_start: 0.2630 (pm20) cc_final: 0.2105 (mp0) REVERT: Q 301 HIS cc_start: 0.4148 (m90) cc_final: 0.3289 (t-90) REVERT: S 35 LYS cc_start: 0.1823 (tttt) cc_final: 0.1225 (ttpt) REVERT: S 386 MET cc_start: 0.3625 (tpp) cc_final: 0.3290 (tpp) REVERT: S 484 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6325 (mmm-85) REVERT: S 693 PHE cc_start: 0.0435 (m-80) cc_final: -0.0954 (p90) REVERT: S 777 MET cc_start: 0.2408 (ttp) cc_final: 0.1860 (tpt) REVERT: R 236 PHE cc_start: 0.3276 (t80) cc_final: 0.2590 (t80) REVERT: R 291 ARG cc_start: 0.3444 (mpt180) cc_final: 0.1394 (tmt-80) REVERT: R 307 LYS cc_start: 0.3137 (mmmt) cc_final: 0.2822 (tttm) REVERT: R 349 ILE cc_start: 0.6884 (tt) cc_final: 0.6439 (mt) REVERT: M 103 LYS cc_start: 0.5399 (mtpp) cc_final: 0.5184 (mmmt) REVERT: A 49 LEU cc_start: 0.6958 (mp) cc_final: 0.6664 (mt) REVERT: A 129 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (pp) REVERT: A 238 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5071 (ppp) REVERT: A 347 ARG cc_start: 0.6972 (ptp90) cc_final: 0.5945 (ttt90) REVERT: A 420 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6462 (t80) REVERT: A 424 MET cc_start: 0.6639 (mmp) cc_final: 0.5660 (ptm) REVERT: A 439 ASP cc_start: 0.7164 (m-30) cc_final: 0.6407 (p0) REVERT: A 555 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8150 (ttmt) REVERT: A 693 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: A 785 GLN cc_start: 0.8429 (mm110) cc_final: 0.7915 (mm110) REVERT: A 937 ASN cc_start: 0.7095 (m110) cc_final: 0.6595 (m110) REVERT: A 1012 LYS cc_start: 0.3467 (OUTLIER) cc_final: 0.2095 (ptmt) REVERT: A 1020 GLN cc_start: 0.7698 (tp40) cc_final: 0.7463 (tp40) REVERT: A 1092 GLU cc_start: 0.7901 (mm-30) cc_final: 0.6979 (tm-30) REVERT: A 1126 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6904 (tptt) REVERT: A 1469 TRP cc_start: 0.7842 (p-90) cc_final: 0.7595 (p-90) REVERT: B 43 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7182 (tt0) REVERT: B 229 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.5360 (t80) REVERT: B 268 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6638 (mm-30) REVERT: B 441 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7202 (mttm) REVERT: B 489 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6861 (mt-10) REVERT: B 606 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.5940 (t0) REVERT: B 924 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8210 (mmtt) REVERT: B 940 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5221 (tp30) REVERT: B 941 THR cc_start: 0.6919 (OUTLIER) cc_final: 0.6596 (t) REVERT: B 943 ILE cc_start: 0.8320 (mt) cc_final: 0.7907 (tp) REVERT: B 1057 MET cc_start: 0.8494 (mmm) cc_final: 0.7999 (ttm) REVERT: B 1151 ILE cc_start: 0.5113 (OUTLIER) cc_final: 0.4826 (pp) REVERT: B 1157 GLN cc_start: 0.6662 (mm-40) cc_final: 0.6402 (mm-40) REVERT: B 1188 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6593 (mm-30) REVERT: C 278 GLU cc_start: 0.6832 (tp30) cc_final: 0.6342 (tp30) REVERT: D 26 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: E 30 ILE cc_start: 0.8019 (mm) cc_final: 0.7656 (mm) REVERT: E 93 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6442 (tpp) REVERT: E 96 PHE cc_start: 0.6851 (t80) cc_final: 0.6136 (t80) REVERT: G 21 LYS cc_start: 0.7401 (mttt) cc_final: 0.6958 (tmmt) REVERT: G 85 GLU cc_start: 0.7076 (tt0) cc_final: 0.6601 (pp20) REVERT: G 110 ASP cc_start: 0.7056 (m-30) cc_final: 0.6828 (t0) REVERT: H 9 ILE cc_start: 0.8729 (mt) cc_final: 0.8491 (mm) REVERT: H 128 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6707 (m-40) REVERT: H 145 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6555 (ttm-80) REVERT: J 2 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6992 (pp) REVERT: J 68 LYS cc_start: 0.7545 (tttp) cc_final: 0.5930 (mmtm) REVERT: K 85 ASP cc_start: 0.8031 (t0) cc_final: 0.7454 (t0) REVERT: L 42 ARG cc_start: 0.6134 (ptt-90) cc_final: 0.5768 (mmt-90) REVERT: N 80 MET cc_start: 0.3924 (ttp) cc_final: 0.3190 (tmm) REVERT: N 107 MET cc_start: 0.5049 (mmm) cc_final: 0.3906 (mmm) REVERT: N 166 LEU cc_start: 0.1072 (OUTLIER) cc_final: 0.0619 (pp) REVERT: O 149 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6879 (tttt) REVERT: O 369 LYS cc_start: 0.8043 (ptpt) cc_final: 0.7810 (tmmt) REVERT: O 382 GLN cc_start: 0.7238 (pm20) cc_final: 0.6579 (mp10) REVERT: O 451 ASN cc_start: 0.5525 (m-40) cc_final: 0.4837 (p0) REVERT: O 467 MET cc_start: 0.6583 (mmm) cc_final: 0.5885 (mmt) REVERT: O 541 PHE cc_start: 0.5910 (t80) cc_final: 0.5586 (t80) REVERT: O 551 ARG cc_start: 0.5950 (mmt180) cc_final: 0.5533 (ptt90) outliers start: 144 outliers final: 118 residues processed: 671 average time/residue: 0.6133 time to fit residues: 694.4224 Evaluate side-chains 707 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 570 time to evaluate : 5.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 108 PHE 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 203 ILE 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 476 ILE Chi-restraints excluded: chain S residue 489 PHE Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 638 LEU Chi-restraints excluded: chain S residue 667 ASP Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 413 THR 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 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 360 LEU Chi-restraints excluded: chain A residue 400 ASN 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 440 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 555 LYS 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 793 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 VAL 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 1224 GLU Chi-restraints excluded: chain A residue 1333 ILE 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 1563 VAL Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS 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 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 606 ASP Chi-restraints excluded: chain B residue 726 MET 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 940 GLU Chi-restraints excluded: chain B residue 941 THR 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 B residue 1199 ASN 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 201 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 159 ASP 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 138 PHE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 128 ASN 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 140 LYS Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain N residue 154 ARG 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 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 386 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 449 optimal weight: 0.0050 chunk 71 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 487 optimal weight: 0.6980 chunk 204 optimal weight: 0.4980 chunk 500 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1314 GLN ** A1454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.211839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.198701 restraints weight = 88095.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.196431 restraints weight = 133328.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.192835 restraints weight = 101901.991| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 52042 Z= 0.192 Angle : 0.648 59.199 70656 Z= 0.344 Chirality : 0.043 0.469 7887 Planarity : 0.004 0.087 8789 Dihedral : 13.085 172.224 7520 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.47 % Favored : 92.51 % Rotamer: Outliers : 2.54 % Allowed : 16.93 % Favored : 80.54 % 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: -2.26 (0.11), residues: 6049 helix: -0.83 (0.11), residues: 2048 sheet: -2.04 (0.19), residues: 675 loop : -1.82 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 316 HIS 0.010 0.001 HIS Q 171 PHE 0.025 0.001 PHE B 376 TYR 0.016 0.001 TYR B1014 ARG 0.021 0.000 ARG H 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13987.80 seconds wall clock time: 253 minutes 18.51 seconds (15198.51 seconds total)