Starting phenix.real_space_refine on Sun Mar 17 07:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc4_19047/03_2024/8rc4_19047.pdb" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 S 396 5.16 5 C 49383 2.51 5 N 13878 2.21 5 O 14612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "p TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 253": "OD1" <-> "OD2" Residue "a ASP 956": "OD1" <-> "OD2" Residue "a GLU 970": "OE1" <-> "OE2" Residue "a ASP 973": "OD1" <-> "OD2" Residue "a TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1077": "OE1" <-> "OE2" Residue "a GLU 1078": "OE1" <-> "OE2" Residue "a PHE 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1211": "OE1" <-> "OE2" Residue "a GLU 1227": "OE1" <-> "OE2" Residue "a ASP 1282": "OD1" <-> "OD2" Residue "a PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 297": "OD1" <-> "OD2" Residue "b ASP 1040": "OD1" <-> "OD2" Residue "d ASP 578": "OD1" <-> "OD2" Residue "d PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 774": "OD1" <-> "OD2" Residue "f PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 876": "OE1" <-> "OE2" Residue "g ASP 912": "OD1" <-> "OD2" Residue "h PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 424": "OE1" <-> "OE2" Residue "i TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78273 Number of models: 1 Model: "" Number of chains: 18 Chain: "p" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4437 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 26, 'TRANS': 553} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "q" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2340 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 263 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "a" Number of atoms: 11842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1766, 11842 Classifications: {'peptide': 1766} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 631} Link IDs: {'PCIS': 4, 'PTRANS': 86, 'TRANS': 1675} Chain breaks: 15 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2259 Unresolved non-hydrogen angles: 2897 Unresolved non-hydrogen dihedrals: 1863 Unresolved non-hydrogen chiralities: 220 Planarities with less than four sites: {'GLN:plan1': 32, 'HIS:plan': 17, 'TYR:plan': 18, 'ASN:plan1': 36, 'TRP:plan': 11, 'ASP:plan': 35, 'PHE:plan': 20, 'GLU:plan': 56, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1190 Chain: "b" Number of atoms: 8099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8099 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 51, 'TRANS': 999} Chain breaks: 9 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 11, 'ARG:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "d" Number of atoms: 6443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6443 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 41, 'TRANS': 781} Chain breaks: 4 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "e" Number of atoms: 6373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6373 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 814} Chain breaks: 7 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 166 Chain: "f" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4422 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 45, 'TRANS': 515} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "g" Number of atoms: 6764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6764 Classifications: {'peptide': 889} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 859} Chain breaks: 4 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Chain: "h" Number of atoms: 7623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7623 Classifications: {'peptide': 956} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 913} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "i" Number of atoms: 4871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4871 Classifications: {'peptide': 626} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 578} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "k" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4411 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 25, 'TRANS': 563} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 164 Chain: "m" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 2810 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PTRANS': 26, 'TRANS': 515} Chain breaks: 6 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 1606 Unresolved non-hydrogen angles: 2057 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 26, 'TYR:plan': 13, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 23, 'PHE:plan': 13, 'GLU:plan': 40, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 852 Chain: "j" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 3238 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 586} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 633} Chain breaks: 3 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2200 Unresolved non-hydrogen angles: 2817 Unresolved non-hydrogen dihedrals: 1837 Unresolved non-hydrogen chiralities: 195 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 17, 'TYR:plan': 23, 'ASN:plan1': 33, 'TRP:plan': 10, 'ASP:plan': 29, 'PHE:plan': 31, 'GLU:plan': 50, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1251 Chain: "n" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 2484 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 438} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 469} Chain breaks: 1 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 1520 Unresolved non-hydrogen angles: 1950 Unresolved non-hydrogen dihedrals: 1261 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 27, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 5, 'HIS:plan': 12, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 773 Chain: "o" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1849 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 336} Link IDs: {'PTRANS': 20, 'TRANS': 351} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1465 Unresolved non-hydrogen dihedrals: 931 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 21, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 13, 'GLU:plan': 18, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 556 Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 30.48, per 1000 atoms: 0.39 Number of scatterers: 78273 At special positions: 0 Unit cell: (208.95, 229.95, 284.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 396 16.00 O 14612 8.00 N 13878 7.00 C 49383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 638 " - pdb=" SG CYS g 778 " 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: 22.41 Conformation dependent library (CDL) restraints added in 11.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN k1001 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 73 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 414 " pdb="ZN ZN k1001 " - pdb="ZN ZN k1002 " pdb=" ZN k1002 " pdb="ZN ZN k1002 " - pdb=" ND1 HIS k 70 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 68 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 157 " 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21242 Finding SS restraints... Secondary structure from input PDB file: 601 helices and 33 sheets defined 65.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'p' and resid 24 through 34 removed outlier: 3.857A pdb=" N ARG p 28 " --> pdb=" O ASP p 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 34 through 42 removed outlier: 3.805A pdb=" N ILE p 38 " --> pdb=" O LYS p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 43 through 58 removed outlier: 4.626A pdb=" N LEU p 52 " --> pdb=" O ARG p 48 " (cutoff:3.500A) Proline residue: p 53 - end of helix Processing helix chain 'p' and resid 62 through 74 removed outlier: 3.570A pdb=" N GLY p 74 " --> pdb=" O ALA p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 88 removed outlier: 4.846A pdb=" N HIS p 87 " --> pdb=" O GLU p 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 98 removed outlier: 3.626A pdb=" N LEU p 93 " --> pdb=" O LEU p 89 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 117 removed outlier: 4.023A pdb=" N HIS p 117 " --> pdb=" O ARG p 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 120 through 127 Processing helix chain 'p' and resid 127 through 137 Processing helix chain 'p' and resid 140 through 149 removed outlier: 3.626A pdb=" N ARG p 144 " --> pdb=" O TRP p 140 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS p 148 " --> pdb=" O ARG p 144 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY p 149 " --> pdb=" O THR p 145 " (cutoff:3.500A) Processing helix chain 'p' and resid 150 through 155 removed outlier: 3.679A pdb=" N CYS p 154 " --> pdb=" O LEU p 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 156 through 158 No H-bonds generated for 'chain 'p' and resid 156 through 158' Processing helix chain 'p' and resid 159 through 175 Processing helix chain 'p' and resid 178 through 196 removed outlier: 4.398A pdb=" N GLY p 190 " --> pdb=" O ALA p 186 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU p 191 " --> pdb=" O SER p 187 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL p 195 " --> pdb=" O GLU p 191 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU p 196 " --> pdb=" O PHE p 192 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 214 removed outlier: 4.086A pdb=" N ILE p 206 " --> pdb=" O LYS p 202 " (cutoff:3.500A) Proline residue: p 207 - end of helix Processing helix chain 'p' and resid 217 through 235 removed outlier: 3.881A pdb=" N ARG p 221 " --> pdb=" O GLN p 217 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL p 229 " --> pdb=" O VAL p 225 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN p 230 " --> pdb=" O GLU p 226 " (cutoff:3.500A) Processing helix chain 'p' and resid 236 through 238 No H-bonds generated for 'chain 'p' and resid 236 through 238' Processing helix chain 'p' and resid 239 through 244 Processing helix chain 'p' and resid 244 through 253 removed outlier: 3.521A pdb=" N GLU p 253 " --> pdb=" O ARG p 249 " (cutoff:3.500A) Processing helix chain 'p' and resid 256 through 266 removed outlier: 3.524A pdb=" N ARG p 260 " --> pdb=" O SER p 256 " (cutoff:3.500A) Processing helix chain 'p' and resid 266 through 275 removed outlier: 3.507A pdb=" N GLY p 275 " --> pdb=" O GLN p 271 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 292 removed outlier: 4.856A pdb=" N VAL p 284 " --> pdb=" O LYS p 280 " (cutoff:3.500A) Proline residue: p 285 - end of helix Processing helix chain 'p' and resid 295 through 304 Processing helix chain 'p' and resid 305 through 312 removed outlier: 3.584A pdb=" N ASN p 312 " --> pdb=" O GLU p 308 " (cutoff:3.500A) Processing helix chain 'p' and resid 313 through 316 removed outlier: 6.104A pdb=" N ASP p 316 " --> pdb=" O LEU p 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 313 through 316' Processing helix chain 'p' and resid 317 through 335 removed outlier: 3.565A pdb=" N VAL p 321 " --> pdb=" O CYS p 317 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU p 327 " --> pdb=" O MET p 323 " (cutoff:3.500A) Proline residue: p 328 - end of helix removed outlier: 3.914A pdb=" N SER p 335 " --> pdb=" O LYS p 331 " (cutoff:3.500A) Processing helix chain 'p' and resid 338 through 350 removed outlier: 3.567A pdb=" N LYS p 342 " --> pdb=" O ASN p 338 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL p 348 " --> pdb=" O ALA p 344 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET p 350 " --> pdb=" O ALA p 346 " (cutoff:3.500A) Processing helix chain 'p' and resid 351 through 357 removed outlier: 4.513A pdb=" N ILE p 355 " --> pdb=" O GLY p 351 " (cutoff:3.500A) Processing helix chain 'p' and resid 357 through 364 Processing helix chain 'p' and resid 364 through 374 removed outlier: 4.007A pdb=" N LEU p 368 " --> pdb=" O HIS p 364 " (cutoff:3.500A) Processing helix chain 'p' and resid 377 through 386 removed outlier: 3.557A pdb=" N ARG p 381 " --> pdb=" O CYS p 377 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER p 386 " --> pdb=" O LEU p 382 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 396 removed outlier: 4.207A pdb=" N VAL p 391 " --> pdb=" O ASN p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 397 through 404 Processing helix chain 'p' and resid 404 through 412 Processing helix chain 'p' and resid 416 through 426 removed outlier: 3.743A pdb=" N ARG p 420 " --> pdb=" O LYS p 416 " (cutoff:3.500A) Processing helix chain 'p' and resid 426 through 433 removed outlier: 3.611A pdb=" N LEU p 430 " --> pdb=" O TYR p 426 " (cutoff:3.500A) Processing helix chain 'p' and resid 435 through 443 Processing helix chain 'p' and resid 443 through 450 Processing helix chain 'p' and resid 451 through 453 No H-bonds generated for 'chain 'p' and resid 451 through 453' Processing helix chain 'p' and resid 455 through 482 removed outlier: 3.641A pdb=" N LYS p 467 " --> pdb=" O THR p 463 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS p 468 " --> pdb=" O SER p 464 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS p 475 " --> pdb=" O GLU p 471 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N GLU p 476 " --> pdb=" O LYS p 472 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TRP p 477 " --> pdb=" O PHE p 473 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 478 " --> pdb=" O GLY p 474 " (cutoff:3.500A) Processing helix chain 'p' and resid 482 through 489 removed outlier: 3.946A pdb=" N MET p 489 " --> pdb=" O LYS p 485 " (cutoff:3.500A) Processing helix chain 'p' and resid 490 through 492 No H-bonds generated for 'chain 'p' and resid 490 through 492' Processing helix chain 'p' and resid 494 through 520 removed outlier: 3.537A pdb=" N ARG p 498 " --> pdb=" O ASN p 494 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU p 510 " --> pdb=" O ASN p 506 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL p 511 " --> pdb=" O VAL p 507 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY p 513 " --> pdb=" O SER p 509 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN p 514 " --> pdb=" O GLU p 510 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASP p 515 " --> pdb=" O VAL p 511 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE p 516 " --> pdb=" O CYS p 512 " (cutoff:3.500A) Processing helix chain 'p' and resid 521 through 527 Processing helix chain 'p' and resid 528 through 531 Processing helix chain 'p' and resid 533 through 547 Processing helix chain 'p' and resid 554 through 568 removed outlier: 4.362A pdb=" N SER p 558 " --> pdb=" O SER p 554 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS p 561 " --> pdb=" O GLN p 557 " (cutoff:3.500A) Proline residue: p 562 - end of helix Processing helix chain 'p' and resid 572 through 587 Processing helix chain 'q' and resid 7 through 18 Processing helix chain 'q' and resid 24 through 40 Processing helix chain 'q' and resid 61 through 73 Processing helix chain 'q' and resid 92 through 107 Processing helix chain 'q' and resid 120 through 127 Processing helix chain 'q' and resid 128 through 138 Processing helix chain 'q' and resid 140 through 151 removed outlier: 3.531A pdb=" N ASP q 151 " --> pdb=" O THR q 147 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 183 removed outlier: 3.751A pdb=" N ILE q 180 " --> pdb=" O THR q 176 " (cutoff:3.500A) Processing helix chain 'q' and resid 193 through 201 removed outlier: 3.624A pdb=" N LEU q 198 " --> pdb=" O PRO q 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU q 199 " --> pdb=" O MET q 195 " (cutoff:3.500A) Processing helix chain 'q' and resid 221 through 233 removed outlier: 3.519A pdb=" N SER q 225 " --> pdb=" O GLY q 221 " (cutoff:3.500A) Processing helix chain 'r' and resid 1048 through 1059 Processing helix chain 'a' and resid 121 through 132 Processing helix chain 'a' and resid 136 through 152 removed outlier: 3.712A pdb=" N GLY a 140 " --> pdb=" O ASP a 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY a 144 " --> pdb=" O GLY a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 169 removed outlier: 3.727A pdb=" N LEU a 162 " --> pdb=" O SER a 158 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET a 165 " --> pdb=" O TYR a 161 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR a 166 " --> pdb=" O LEU a 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS a 169 " --> pdb=" O MET a 165 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 176 Processing helix chain 'a' and resid 177 through 188 removed outlier: 4.280A pdb=" N ILE a 181 " --> pdb=" O THR a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 213 removed outlier: 3.627A pdb=" N MET a 213 " --> pdb=" O CYS a 209 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 217 removed outlier: 3.652A pdb=" N GLU a 217 " --> pdb=" O ALA a 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 214 through 217' Processing helix chain 'a' and resid 223 through 234 removed outlier: 3.639A pdb=" N SER a 234 " --> pdb=" O TYR a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 257 removed outlier: 3.575A pdb=" N PHE a 257 " --> pdb=" O ILE a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 321 through 338 removed outlier: 4.251A pdb=" N ASP a 335 " --> pdb=" O ASP a 331 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN a 336 " --> pdb=" O MET a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 349 through 357 removed outlier: 4.349A pdb=" N LEU a 353 " --> pdb=" O ASN a 349 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR a 357 " --> pdb=" O LEU a 353 " (cutoff:3.500A) Processing helix chain 'a' and resid 360 through 370 removed outlier: 3.757A pdb=" N LYS a 370 " --> pdb=" O LEU a 366 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 379 No H-bonds generated for 'chain 'a' and resid 377 through 379' Processing helix chain 'a' and resid 380 through 395 Processing helix chain 'a' and resid 399 through 411 removed outlier: 3.937A pdb=" N LYS a 411 " --> pdb=" O SER a 407 " (cutoff:3.500A) Processing helix chain 'a' and resid 416 through 434 removed outlier: 4.138A pdb=" N LEU a 420 " --> pdb=" O PRO a 416 " (cutoff:3.500A) Processing helix chain 'a' and resid 436 through 451 removed outlier: 3.738A pdb=" N THR a 440 " --> pdb=" O ASP a 436 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE a 446 " --> pdb=" O ILE a 442 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE a 447 " --> pdb=" O LYS a 443 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU a 450 " --> pdb=" O ILE a 446 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 469 removed outlier: 3.729A pdb=" N MET a 459 " --> pdb=" O ASN a 455 " (cutoff:3.500A) Processing helix chain 'a' and resid 472 through 485 removed outlier: 3.617A pdb=" N PHE a 476 " --> pdb=" O LEU a 472 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET a 479 " --> pdb=" O LYS a 475 " (cutoff:3.500A) Processing helix chain 'a' and resid 491 through 506 Processing helix chain 'a' and resid 513 through 521 removed outlier: 3.610A pdb=" N LEU a 517 " --> pdb=" O GLN a 513 " (cutoff:3.500A) Processing helix chain 'a' and resid 525 through 530 removed outlier: 3.743A pdb=" N LEU a 529 " --> pdb=" O GLU a 525 " (cutoff:3.500A) Processing helix chain 'a' and resid 534 through 550 removed outlier: 3.718A pdb=" N VAL a 538 " --> pdb=" O LYS a 534 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET a 550 " --> pdb=" O ALA a 546 " (cutoff:3.500A) Processing helix chain 'a' and resid 551 through 553 No H-bonds generated for 'chain 'a' and resid 551 through 553' Processing helix chain 'a' and resid 554 through 564 Processing helix chain 'a' and resid 572 through 585 Processing helix chain 'a' and resid 588 through 595 Processing helix chain 'a' and resid 596 through 601 Processing helix chain 'a' and resid 604 through 615 Processing helix chain 'a' and resid 620 through 626 removed outlier: 3.868A pdb=" N TYR a 625 " --> pdb=" O GLU a 622 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS a 626 " --> pdb=" O THR a 623 " (cutoff:3.500A) Processing helix chain 'a' and resid 635 through 645 removed outlier: 3.669A pdb=" N ARG a 641 " --> pdb=" O ASN a 637 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU a 642 " --> pdb=" O PHE a 638 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU a 645 " --> pdb=" O ARG a 641 " (cutoff:3.500A) Processing helix chain 'a' and resid 650 through 662 Processing helix chain 'a' and resid 668 through 684 removed outlier: 4.587A pdb=" N ALA a 672 " --> pdb=" O GLY a 668 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA a 684 " --> pdb=" O VAL a 680 " (cutoff:3.500A) Processing helix chain 'a' and resid 700 through 710 Processing helix chain 'a' and resid 730 through 748 Proline residue: a 739 - end of helix Processing helix chain 'a' and resid 751 through 760 removed outlier: 4.363A pdb=" N ALA a 755 " --> pdb=" O ASN a 751 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA a 756 " --> pdb=" O ILE a 752 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU a 758 " --> pdb=" O LEU a 754 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU a 759 " --> pdb=" O ALA a 755 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR a 760 " --> pdb=" O ALA a 756 " (cutoff:3.500A) Processing helix chain 'a' and resid 760 through 772 removed outlier: 4.250A pdb=" N LYS a 764 " --> pdb=" O TYR a 760 " (cutoff:3.500A) Processing helix chain 'a' and resid 788 through 819 removed outlier: 3.749A pdb=" N GLN a 797 " --> pdb=" O ASN a 793 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR a 798 " --> pdb=" O ARG a 794 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE a 809 " --> pdb=" O GLU a 805 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU a 810 " --> pdb=" O ILE a 806 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS a 812 " --> pdb=" O ALA a 808 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU a 813 " --> pdb=" O PHE a 809 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER a 817 " --> pdb=" O LEU a 813 " (cutoff:3.500A) Processing helix chain 'a' and resid 827 through 831 Processing helix chain 'a' and resid 846 through 861 removed outlier: 3.810A pdb=" N SER a 855 " --> pdb=" O ASP a 851 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU a 856 " --> pdb=" O GLN a 852 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN a 858 " --> pdb=" O LYS a 854 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER a 859 " --> pdb=" O SER a 855 " (cutoff:3.500A) Processing helix chain 'a' and resid 947 through 959 Processing helix chain 'a' and resid 964 through 977 removed outlier: 3.596A pdb=" N THR a 968 " --> pdb=" O ASP a 964 " (cutoff:3.500A) Processing helix chain 'a' and resid 983 through 999 Processing helix chain 'a' and resid 1023 through 1025 No H-bonds generated for 'chain 'a' and resid 1023 through 1025' Processing helix chain 'a' and resid 1026 through 1032 removed outlier: 3.748A pdb=" N LEU a1030 " --> pdb=" O TYR a1026 " (cutoff:3.500A) Processing helix chain 'a' and resid 1033 through 1036 Processing helix chain 'a' and resid 1038 through 1055 removed outlier: 4.754A pdb=" N SER a1044 " --> pdb=" O ASP a1040 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR a1045 " --> pdb=" O SER a1041 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS a1055 " --> pdb=" O GLN a1051 " (cutoff:3.500A) Processing helix chain 'a' and resid 1059 through 1073 Processing helix chain 'a' and resid 1078 through 1096 Processing helix chain 'a' and resid 1096 through 1104 Processing helix chain 'a' and resid 1110 through 1134 Processing helix chain 'a' and resid 1163 through 1176 removed outlier: 3.939A pdb=" N VAL a1167 " --> pdb=" O HIS a1163 " (cutoff:3.500A) Processing helix chain 'a' and resid 1183 through 1194 Processing helix chain 'a' and resid 1216 through 1225 Processing helix chain 'a' and resid 1228 through 1236 removed outlier: 3.619A pdb=" N VAL a1232 " --> pdb=" O VAL a1228 " (cutoff:3.500A) Processing helix chain 'a' and resid 1240 through 1250 Processing helix chain 'a' and resid 1254 through 1272 Processing helix chain 'a' and resid 1273 through 1276 removed outlier: 3.836A pdb=" N LEU a1276 " --> pdb=" O PRO a1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1273 through 1276' Processing helix chain 'a' and resid 1283 through 1297 Processing helix chain 'a' and resid 1301 through 1312 removed outlier: 3.669A pdb=" N SER a1311 " --> pdb=" O LEU a1307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU a1312 " --> pdb=" O LEU a1308 " (cutoff:3.500A) Processing helix chain 'a' and resid 1361 through 1369 Processing helix chain 'a' and resid 1374 through 1393 Processing helix chain 'a' and resid 1402 through 1415 Processing helix chain 'a' and resid 1421 through 1428 Processing helix chain 'a' and resid 1428 through 1446 Proline residue: a1434 - end of helix Processing helix chain 'a' and resid 1451 through 1468 Processing helix chain 'a' and resid 1469 through 1473 removed outlier: 3.556A pdb=" N VAL a1472 " --> pdb=" O SER a1469 " (cutoff:3.500A) Processing helix chain 'a' and resid 1475 through 1490 removed outlier: 3.570A pdb=" N ALA a1479 " --> pdb=" O GLY a1475 " (cutoff:3.500A) Processing helix chain 'a' and resid 1496 through 1511 Processing helix chain 'a' and resid 1513 through 1531 Processing helix chain 'a' and resid 1537 through 1552 Processing helix chain 'a' and resid 1555 through 1566 removed outlier: 3.931A pdb=" N ALA a1566 " --> pdb=" O ALA a1562 " (cutoff:3.500A) Processing helix chain 'a' and resid 1579 through 1589 Processing helix chain 'a' and resid 1614 through 1626 Processing helix chain 'a' and resid 1633 through 1642 removed outlier: 3.622A pdb=" N GLN a1637 " --> pdb=" O CYS a1633 " (cutoff:3.500A) Processing helix chain 'a' and resid 1656 through 1668 Processing helix chain 'a' and resid 1669 through 1681 Processing helix chain 'a' and resid 1690 through 1703 Processing helix chain 'a' and resid 1728 through 1747 Processing helix chain 'a' and resid 1755 through 1770 removed outlier: 3.548A pdb=" N GLN a1759 " --> pdb=" O CYS a1755 " (cutoff:3.500A) Proline residue: a1763 - end of helix Processing helix chain 'a' and resid 1772 through 1791 removed outlier: 3.573A pdb=" N VAL a1776 " --> pdb=" O ASP a1772 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS a1778 " --> pdb=" O GLU a1774 " (cutoff:3.500A) Processing helix chain 'a' and resid 1793 through 1810 Processing helix chain 'a' and resid 1818 through 1823 Processing helix chain 'a' and resid 1835 through 1848 removed outlier: 3.583A pdb=" N ASP a1848 " --> pdb=" O THR a1844 " (cutoff:3.500A) Processing helix chain 'a' and resid 1852 through 1854 No H-bonds generated for 'chain 'a' and resid 1852 through 1854' Processing helix chain 'a' and resid 1855 through 1873 Processing helix chain 'a' and resid 1873 through 1879 removed outlier: 3.522A pdb=" N LEU a1877 " --> pdb=" O HIS a1873 " (cutoff:3.500A) Processing helix chain 'a' and resid 1880 through 1888 removed outlier: 3.571A pdb=" N ILE a1884 " --> pdb=" O HIS a1880 " (cutoff:3.500A) Processing helix chain 'a' and resid 1889 through 1891 No H-bonds generated for 'chain 'a' and resid 1889 through 1891' Processing helix chain 'a' and resid 1895 through 1902 Processing helix chain 'a' and resid 1904 through 1919 removed outlier: 3.653A pdb=" N PHE a1908 " --> pdb=" O HIS a1904 " (cutoff:3.500A) Processing helix chain 'a' and resid 1920 through 1924 removed outlier: 3.536A pdb=" N ARG a1924 " --> pdb=" O HIS a1921 " (cutoff:3.500A) Processing helix chain 'a' and resid 1928 through 1945 Processing helix chain 'a' and resid 1949 through 1951 No H-bonds generated for 'chain 'a' and resid 1949 through 1951' Processing helix chain 'a' and resid 1952 through 1970 Processing helix chain 'a' and resid 1970 through 1981 Processing helix chain 'a' and resid 1981 through 1992 removed outlier: 3.562A pdb=" N LEU a1985 " --> pdb=" O HIS a1981 " (cutoff:3.500A) Processing helix chain 'a' and resid 1995 through 2003 Processing helix chain 'a' and resid 2004 through 2007 removed outlier: 4.128A pdb=" N LEU a2007 " --> pdb=" O GLY a2004 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2004 through 2007' Processing helix chain 'a' and resid 2047 through 2057 Processing helix chain 'a' and resid 2059 through 2077 Processing helix chain 'a' and resid 2078 through 2083 removed outlier: 3.759A pdb=" N SER a2082 " --> pdb=" O GLU a2079 " (cutoff:3.500A) Processing helix chain 'a' and resid 2084 through 2092 Processing helix chain 'a' and resid 2096 through 2114 Processing helix chain 'a' and resid 2115 through 2120 removed outlier: 4.322A pdb=" N ALA a2119 " --> pdb=" O SER a2116 " (cutoff:3.500A) Processing helix chain 'a' and resid 2121 through 2130 Processing helix chain 'a' and resid 2133 through 2143 Processing helix chain 'a' and resid 2143 through 2152 Processing helix chain 'a' and resid 2154 through 2169 Processing helix chain 'a' and resid 2173 through 2189 Processing helix chain 'b' and resid 19 through 29 Processing helix chain 'b' and resid 30 through 36 Processing helix chain 'b' and resid 38 through 45 removed outlier: 3.783A pdb=" N LEU b 44 " --> pdb=" O PRO b 40 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU b 45 " --> pdb=" O GLU b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 55 Processing helix chain 'b' and resid 61 through 77 removed outlier: 4.268A pdb=" N GLY b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 89 removed outlier: 3.890A pdb=" N ILE b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 107 removed outlier: 3.629A pdb=" N LEU b 95 " --> pdb=" O ASP b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 133 Processing helix chain 'b' and resid 134 through 156 Processing helix chain 'b' and resid 173 through 188 Processing helix chain 'b' and resid 193 through 202 removed outlier: 3.557A pdb=" N LEU b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 218 Processing helix chain 'b' and resid 221 through 233 Processing helix chain 'b' and resid 240 through 257 Processing helix chain 'b' and resid 260 through 272 Processing helix chain 'b' and resid 274 through 287 Processing helix chain 'b' and resid 296 through 308 Processing helix chain 'b' and resid 310 through 326 removed outlier: 3.632A pdb=" N GLN b 326 " --> pdb=" O ARG b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.753A pdb=" N GLN b 338 " --> pdb=" O SER b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 381 through 398 Processing helix chain 'b' and resid 404 through 416 Processing helix chain 'b' and resid 422 through 439 Processing helix chain 'b' and resid 440 through 443 Processing helix chain 'b' and resid 445 through 462 Processing helix chain 'b' and resid 476 through 490 Processing helix chain 'b' and resid 491 through 504 Processing helix chain 'b' and resid 511 through 525 Processing helix chain 'b' and resid 527 through 537 removed outlier: 3.914A pdb=" N ARG b 537 " --> pdb=" O ALA b 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 552 through 564 removed outlier: 3.509A pdb=" N CYS b 556 " --> pdb=" O LEU b 552 " (cutoff:3.500A) Processing helix chain 'b' and resid 573 through 582 Processing helix chain 'b' and resid 591 through 604 Processing helix chain 'b' and resid 620 through 626 Processing helix chain 'b' and resid 644 through 665 Processing helix chain 'b' and resid 666 through 669 removed outlier: 3.908A pdb=" N LEU b 669 " --> pdb=" O THR b 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 666 through 669' Processing helix chain 'b' and resid 680 through 687 Processing helix chain 'b' and resid 688 through 699 Processing helix chain 'b' and resid 700 through 704 removed outlier: 3.933A pdb=" N GLY b 704 " --> pdb=" O GLN b 701 " (cutoff:3.500A) Processing helix chain 'b' and resid 705 through 718 Processing helix chain 'b' and resid 719 through 722 Processing helix chain 'b' and resid 723 through 729 removed outlier: 3.810A pdb=" N CYS b 729 " --> pdb=" O ASP b 725 " (cutoff:3.500A) Processing helix chain 'b' and resid 735 through 745 Processing helix chain 'b' and resid 746 through 748 No H-bonds generated for 'chain 'b' and resid 746 through 748' Processing helix chain 'b' and resid 753 through 762 Processing helix chain 'b' and resid 767 through 779 removed outlier: 3.592A pdb=" N ILE b 774 " --> pdb=" O GLN b 770 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS b 777 " --> pdb=" O GLN b 773 " (cutoff:3.500A) Processing helix chain 'b' and resid 783 through 788 removed outlier: 3.660A pdb=" N ILE b 787 " --> pdb=" O SER b 784 " (cutoff:3.500A) Proline residue: b 788 - end of helix Processing helix chain 'b' and resid 789 through 796 Processing helix chain 'b' and resid 797 through 802 Processing helix chain 'b' and resid 806 through 822 Processing helix chain 'b' and resid 824 through 836 Processing helix chain 'b' and resid 849 through 856 Processing helix chain 'b' and resid 857 through 862 Processing helix chain 'b' and resid 864 through 869 Processing helix chain 'b' and resid 870 through 901 removed outlier: 4.400A pdb=" N GLN b 901 " --> pdb=" O LYS b 897 " (cutoff:3.500A) Processing helix chain 'b' and resid 923 through 946 Processing helix chain 'b' and resid 949 through 954 Processing helix chain 'b' and resid 988 through 1008 removed outlier: 3.535A pdb=" N GLU b 992 " --> pdb=" O CYS b 988 " (cutoff:3.500A) Processing helix chain 'b' and resid 1008 through 1019 removed outlier: 3.852A pdb=" N ALA b1012 " --> pdb=" O ASP b1008 " (cutoff:3.500A) Processing helix chain 'b' and resid 1021 through 1023 No H-bonds generated for 'chain 'b' and resid 1021 through 1023' Processing helix chain 'b' and resid 1024 through 1032 Processing helix chain 'b' and resid 1033 through 1036 removed outlier: 3.816A pdb=" N HIS b1036 " --> pdb=" O PRO b1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1033 through 1036' Processing helix chain 'b' and resid 1037 through 1047 removed outlier: 4.101A pdb=" N PHE b1041 " --> pdb=" O ILE b1037 " (cutoff:3.500A) Proline residue: b1043 - end of helix Processing helix chain 'b' and resid 1050 through 1068 Processing helix chain 'b' and resid 1070 through 1089 removed outlier: 4.048A pdb=" N THR b1089 " --> pdb=" O GLY b1085 " (cutoff:3.500A) Processing helix chain 'b' and resid 1092 through 1104 Proline residue: b1102 - end of helix Processing helix chain 'b' and resid 1105 through 1114 removed outlier: 3.850A pdb=" N SER b1109 " --> pdb=" O PRO b1105 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1139 removed outlier: 3.959A pdb=" N GLN b1139 " --> pdb=" O ASP b1135 " (cutoff:3.500A) Processing helix chain 'b' and resid 1144 through 1149 removed outlier: 3.935A pdb=" N THR b1148 " --> pdb=" O ASP b1144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG b1149 " --> pdb=" O PRO b1145 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1144 through 1149' Processing helix chain 'b' and resid 1180 through 1200 Processing helix chain 'd' and resid 36 through 46 Processing helix chain 'd' and resid 50 through 62 removed outlier: 3.713A pdb=" N ARG d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS d 62 " --> pdb=" O GLN d 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 Processing helix chain 'd' and resid 85 through 99 Processing helix chain 'd' and resid 100 through 102 No H-bonds generated for 'chain 'd' and resid 100 through 102' Processing helix chain 'd' and resid 106 through 110 removed outlier: 4.185A pdb=" N CYS d 109 " --> pdb=" O SER d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 121 Processing helix chain 'd' and resid 123 through 141 Processing helix chain 'd' and resid 144 through 158 removed outlier: 3.849A pdb=" N GLN d 148 " --> pdb=" O ASN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 163 through 177 Processing helix chain 'd' and resid 196 through 202 Processing helix chain 'd' and resid 203 through 206 removed outlier: 3.552A pdb=" N ASP d 206 " --> pdb=" O TYR d 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 203 through 206' Processing helix chain 'd' and resid 208 through 226 Processing helix chain 'd' and resid 231 through 241 removed outlier: 4.329A pdb=" N ASN d 235 " --> pdb=" O GLN d 231 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN d 236 " --> pdb=" O THR d 232 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU d 240 " --> pdb=" O GLN d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 263 Processing helix chain 'd' and resid 279 through 290 Processing helix chain 'd' and resid 291 through 293 No H-bonds generated for 'chain 'd' and resid 291 through 293' Processing helix chain 'd' and resid 295 through 309 Processing helix chain 'd' and resid 313 through 320 removed outlier: 3.765A pdb=" N THR d 320 " --> pdb=" O PHE d 316 " (cutoff:3.500A) Processing helix chain 'd' and resid 377 through 384 removed outlier: 3.771A pdb=" N GLU d 384 " --> pdb=" O VAL d 380 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 405 removed outlier: 3.690A pdb=" N ARG d 391 " --> pdb=" O MET d 387 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 419 removed outlier: 3.608A pdb=" N LYS d 411 " --> pdb=" O SER d 407 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP d 414 " --> pdb=" O GLU d 410 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE d 415 " --> pdb=" O LYS d 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 420 through 422 No H-bonds generated for 'chain 'd' and resid 420 through 422' Processing helix chain 'd' and resid 424 through 438 Processing helix chain 'd' and resid 439 through 442 removed outlier: 3.604A pdb=" N ILE d 442 " --> pdb=" O SER d 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 439 through 442' Processing helix chain 'd' and resid 445 through 455 Processing helix chain 'd' and resid 460 through 474 Processing helix chain 'd' and resid 478 through 496 Processing helix chain 'd' and resid 499 through 514 removed outlier: 3.554A pdb=" N SER d 512 " --> pdb=" O LYS d 508 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG d 513 " --> pdb=" O PHE d 509 " (cutoff:3.500A) Processing helix chain 'd' and resid 514 through 527 Proline residue: d 520 - end of helix Proline residue: d 523 - end of helix removed outlier: 3.744A pdb=" N SER d 527 " --> pdb=" O PRO d 523 " (cutoff:3.500A) Processing helix chain 'd' and resid 541 through 556 Processing helix chain 'd' and resid 559 through 564 removed outlier: 4.202A pdb=" N ALA d 563 " --> pdb=" O PRO d 559 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU d 564 " --> pdb=" O THR d 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 559 through 564' Processing helix chain 'd' and resid 566 through 580 removed outlier: 3.694A pdb=" N ASP d 578 " --> pdb=" O ALA d 574 " (cutoff:3.500A) Processing helix chain 'd' and resid 609 through 624 Processing helix chain 'd' and resid 628 through 650 Processing helix chain 'd' and resid 653 through 680 Processing helix chain 'd' and resid 682 through 686 Processing helix chain 'd' and resid 692 through 710 Processing helix chain 'd' and resid 715 through 741 removed outlier: 4.099A pdb=" N ILE d 721 " --> pdb=" O LYS d 717 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR d 740 " --> pdb=" O VAL d 736 " (cutoff:3.500A) Processing helix chain 'd' and resid 743 through 765 removed outlier: 3.836A pdb=" N LEU d 747 " --> pdb=" O GLY d 743 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 772 removed outlier: 3.742A pdb=" N LEU d 769 " --> pdb=" O ILE d 766 " (cutoff:3.500A) Proline residue: d 770 - end of helix No H-bonds generated for 'chain 'd' and resid 766 through 772' Processing helix chain 'd' and resid 775 through 783 removed outlier: 3.522A pdb=" N LEU d 783 " --> pdb=" O LYS d 779 " (cutoff:3.500A) Processing helix chain 'd' and resid 783 through 790 Processing helix chain 'd' and resid 791 through 805 Processing helix chain 'd' and resid 856 through 860 removed outlier: 3.630A pdb=" N THR d 860 " --> pdb=" O ASP d 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 856 through 860' Processing helix chain 'e' and resid 30 through 41 removed outlier: 3.656A pdb=" N GLY e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 66 Processing helix chain 'e' and resid 67 through 69 No H-bonds generated for 'chain 'e' and resid 67 through 69' Processing helix chain 'e' and resid 70 through 93 removed outlier: 4.103A pdb=" N ASP e 75 " --> pdb=" O ALA e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 120 No H-bonds generated for 'chain 'e' and resid 118 through 120' Processing helix chain 'e' and resid 121 through 136 Processing helix chain 'e' and resid 136 through 159 removed outlier: 3.763A pdb=" N TRP e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) Proline residue: e 142 - end of helix Processing helix chain 'e' and resid 172 through 181 removed outlier: 4.117A pdb=" N MET e 181 " --> pdb=" O LEU e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 204 removed outlier: 3.965A pdb=" N ARG e 187 " --> pdb=" O CYS e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 219 removed outlier: 4.190A pdb=" N ASP e 210 " --> pdb=" O ASP e 206 " (cutoff:3.500A) Processing helix chain 'e' and resid 223 through 234 removed outlier: 4.056A pdb=" N VAL e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 234 through 254 removed outlier: 3.792A pdb=" N ILE e 238 " --> pdb=" O PHE e 234 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 303 Processing helix chain 'e' and resid 307 through 320 Processing helix chain 'e' and resid 339 through 348 Processing helix chain 'e' and resid 354 through 362 Processing helix chain 'e' and resid 365 through 376 removed outlier: 6.315A pdb=" N GLN e 371 " --> pdb=" O ALA e 367 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU e 372 " --> pdb=" O VAL e 368 " (cutoff:3.500A) Processing helix chain 'e' and resid 380 through 399 Processing helix chain 'e' and resid 402 through 415 Processing helix chain 'e' and resid 429 through 451 Processing helix chain 'e' and resid 471 through 478 Processing helix chain 'e' and resid 480 through 489 Processing helix chain 'e' and resid 494 through 510 removed outlier: 3.824A pdb=" N TRP e 498 " --> pdb=" O LYS e 494 " (cutoff:3.500A) Processing helix chain 'e' and resid 514 through 526 Processing helix chain 'e' and resid 528 through 544 removed outlier: 3.702A pdb=" N LEU e 534 " --> pdb=" O GLU e 530 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA e 535 " --> pdb=" O GLU e 531 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL e 544 " --> pdb=" O ALA e 540 " (cutoff:3.500A) Processing helix chain 'e' and resid 548 through 563 removed outlier: 3.590A pdb=" N LEU e 552 " --> pdb=" O GLY e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 567 through 587 Processing helix chain 'e' and resid 589 through 596 removed outlier: 3.842A pdb=" N ALA e 593 " --> pdb=" O GLY e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 598 through 604 Processing helix chain 'e' and resid 606 through 611 Processing helix chain 'e' and resid 612 through 616 Processing helix chain 'e' and resid 618 through 632 removed outlier: 3.808A pdb=" N ILE e 631 " --> pdb=" O SER e 627 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 663 Processing helix chain 'e' and resid 664 through 666 No H-bonds generated for 'chain 'e' and resid 664 through 666' Processing helix chain 'e' and resid 667 through 681 removed outlier: 4.306A pdb=" N SER e 681 " --> pdb=" O LEU e 677 " (cutoff:3.500A) Processing helix chain 'e' and resid 681 through 697 Processing helix chain 'e' and resid 702 through 706 removed outlier: 3.572A pdb=" N GLY e 706 " --> pdb=" O GLU e 703 " (cutoff:3.500A) Processing helix chain 'e' and resid 727 through 735 Processing helix chain 'e' and resid 768 through 788 Processing helix chain 'e' and resid 805 through 821 Processing helix chain 'e' and resid 833 through 839 Processing helix chain 'e' and resid 840 through 854 Processing helix chain 'e' and resid 855 through 867 removed outlier: 3.938A pdb=" N GLU e 859 " --> pdb=" O PRO e 855 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA e 867 " --> pdb=" O LEU e 863 " (cutoff:3.500A) Processing helix chain 'e' and resid 868 through 873 removed outlier: 3.553A pdb=" N LEU e 871 " --> pdb=" O PRO e 868 " (cutoff:3.500A) Processing helix chain 'e' and resid 874 through 892 Processing helix chain 'e' and resid 900 through 917 Processing helix chain 'e' and resid 926 through 934 removed outlier: 3.508A pdb=" N PHE e 931 " --> pdb=" O HIS e 928 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER e 932 " --> pdb=" O GLU e 929 " (cutoff:3.500A) Processing helix chain 'e' and resid 935 through 953 Processing helix chain 'e' and resid 956 through 960 Processing helix chain 'e' and resid 973 through 977 removed outlier: 3.600A pdb=" N GLY e 977 " --> pdb=" O SER e 974 " (cutoff:3.500A) Processing helix chain 'e' and resid 981 through 995 removed outlier: 4.095A pdb=" N VAL e 987 " --> pdb=" O PRO e 983 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU e 988 " --> pdb=" O HIS e 984 " (cutoff:3.500A) Processing helix chain 'e' and resid 995 through 1000 Processing helix chain 'e' and resid 1001 through 1007 removed outlier: 4.152A pdb=" N GLY e1004 " --> pdb=" O LEU e1001 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN e1007 " --> pdb=" O GLY e1004 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 16 Processing helix chain 'f' and resid 23 through 40 Processing helix chain 'f' and resid 41 through 46 removed outlier: 6.135A pdb=" N ALA f 44 " --> pdb=" O ARG f 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG f 46 " --> pdb=" O PRO f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 61 Processing helix chain 'f' and resid 69 through 79 Processing helix chain 'f' and resid 87 through 100 Processing helix chain 'f' and resid 102 through 107 Processing helix chain 'f' and resid 154 through 158 removed outlier: 3.526A pdb=" N THR f 158 " --> pdb=" O SER f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 204 removed outlier: 4.655A pdb=" N MET f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 226 Processing helix chain 'f' and resid 332 through 342 Processing helix chain 'f' and resid 385 through 399 Proline residue: f 391 - end of helix removed outlier: 3.815A pdb=" N PHE f 397 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 418 removed outlier: 3.756A pdb=" N THR f 418 " --> pdb=" O SER f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 420 through 422 No H-bonds generated for 'chain 'f' and resid 420 through 422' Processing helix chain 'f' and resid 423 through 435 Processing helix chain 'f' and resid 436 through 440 removed outlier: 4.544A pdb=" N ILE f 440 " --> pdb=" O PRO f 437 " (cutoff:3.500A) Processing helix chain 'f' and resid 449 through 474 Processing helix chain 'f' and resid 543 through 547 removed outlier: 3.570A pdb=" N ASP f 546 " --> pdb=" O ASN f 543 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE f 547 " --> pdb=" O ALA f 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 543 through 547' Processing helix chain 'f' and resid 551 through 565 Processing helix chain 'f' and resid 583 through 587 Processing helix chain 'f' and resid 589 through 596 removed outlier: 3.922A pdb=" N LYS f 595 " --> pdb=" O GLN f 591 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN f 596 " --> pdb=" O GLU f 592 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 34 removed outlier: 3.730A pdb=" N GLY g 32 " --> pdb=" O GLU g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 55 Proline residue: g 49 - end of helix Processing helix chain 'g' and resid 57 through 75 Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 92 through 97 removed outlier: 3.801A pdb=" N GLU g 95 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE g 97 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 109 Processing helix chain 'g' and resid 110 through 113 Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 136 through 148 removed outlier: 4.068A pdb=" N ASP g 148 " --> pdb=" O ARG g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 151 through 169 Processing helix chain 'g' and resid 169 through 186 removed outlier: 3.545A pdb=" N ALA g 173 " --> pdb=" O SER g 169 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN g 178 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS g 179 " --> pdb=" O GLY g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 198 Processing helix chain 'g' and resid 199 through 204 Processing helix chain 'g' and resid 207 through 225 Processing helix chain 'g' and resid 227 through 246 Processing helix chain 'g' and resid 248 through 263 Processing helix chain 'g' and resid 265 through 283 Processing helix chain 'g' and resid 284 through 287 Processing helix chain 'g' and resid 288 through 301 Processing helix chain 'g' and resid 304 through 320 Processing helix chain 'g' and resid 322 through 328 Processing helix chain 'g' and resid 342 through 352 Processing helix chain 'g' and resid 356 through 374 Processing helix chain 'g' and resid 376 through 379 removed outlier: 3.532A pdb=" N LEU g 379 " --> pdb=" O GLU g 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 376 through 379' Processing helix chain 'g' and resid 380 through 399 removed outlier: 4.454A pdb=" N GLN g 384 " --> pdb=" O LEU g 380 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP g 385 " --> pdb=" O ALA g 381 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN g 399 " --> pdb=" O VAL g 395 " (cutoff:3.500A) Processing helix chain 'g' and resid 402 through 423 Processing helix chain 'g' and resid 426 through 439 removed outlier: 3.904A pdb=" N HIS g 439 " --> pdb=" O LEU g 435 " (cutoff:3.500A) Processing helix chain 'g' and resid 442 through 460 Processing helix chain 'g' and resid 461 through 466 removed outlier: 3.871A pdb=" N ASP g 465 " --> pdb=" O VAL g 462 " (cutoff:3.500A) Processing helix chain 'g' and resid 467 through 480 removed outlier: 3.620A pdb=" N ARG g 480 " --> pdb=" O LYS g 476 " (cutoff:3.500A) Processing helix chain 'g' and resid 485 through 501 removed outlier: 3.513A pdb=" N LEU g 489 " --> pdb=" O LYS g 485 " (cutoff:3.500A) Processing helix chain 'g' and resid 506 through 520 removed outlier: 3.681A pdb=" N LYS g 510 " --> pdb=" O SER g 506 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER g 519 " --> pdb=" O GLN g 515 " (cutoff:3.500A) Processing helix chain 'g' and resid 522 through 536 removed outlier: 3.557A pdb=" N VAL g 526 " --> pdb=" O ASN g 522 " (cutoff:3.500A) Processing helix chain 'g' and resid 538 through 550 Processing helix chain 'g' and resid 555 through 575 removed outlier: 3.668A pdb=" N LEU g 575 " --> pdb=" O ALA g 571 " (cutoff:3.500A) Processing helix chain 'g' and resid 582 through 608 Processing helix chain 'g' and resid 614 through 626 Processing helix chain 'g' and resid 628 through 641 removed outlier: 3.743A pdb=" N LEU g 641 " --> pdb=" O THR g 637 " (cutoff:3.500A) Processing helix chain 'g' and resid 646 through 651 Processing helix chain 'g' and resid 661 through 664 Processing helix chain 'g' and resid 665 through 691 removed outlier: 4.062A pdb=" N ASN g 669 " --> pdb=" O GLY g 665 " (cutoff:3.500A) Processing helix chain 'g' and resid 696 through 721 Processing helix chain 'g' and resid 742 through 761 Processing helix chain 'g' and resid 770 through 787 removed outlier: 3.779A pdb=" N THR g 774 " --> pdb=" O SER g 770 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL g 787 " --> pdb=" O ALA g 783 " (cutoff:3.500A) Processing helix chain 'g' and resid 792 through 797 removed outlier: 3.835A pdb=" N PHE g 796 " --> pdb=" O GLN g 792 " (cutoff:3.500A) Processing helix chain 'g' and resid 933 through 945 Processing helix chain 'h' and resid 24 through 30 removed outlier: 3.810A pdb=" N LEU h 28 " --> pdb=" O TRP h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 39 Processing helix chain 'h' and resid 46 through 60 Processing helix chain 'h' and resid 75 through 92 Processing helix chain 'h' and resid 95 through 103 Processing helix chain 'h' and resid 104 through 119 Processing helix chain 'h' and resid 136 through 159 Processing helix chain 'h' and resid 170 through 194 removed outlier: 4.085A pdb=" N GLN h 176 " --> pdb=" O SER h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 194 through 206 Processing helix chain 'h' and resid 216 through 225 removed outlier: 4.324A pdb=" N MET h 225 " --> pdb=" O ASP h 221 " (cutoff:3.500A) Processing helix chain 'h' and resid 244 through 265 removed outlier: 3.918A pdb=" N SER h 265 " --> pdb=" O PHE h 261 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 269 removed outlier: 6.759A pdb=" N ALA h 269 " --> pdb=" O THR h 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 266 through 269' Processing helix chain 'h' and resid 270 through 289 Processing helix chain 'h' and resid 298 through 313 Processing helix chain 'h' and resid 324 through 336 Processing helix chain 'h' and resid 337 through 352 removed outlier: 3.816A pdb=" N LEU h 350 " --> pdb=" O ILE h 346 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR h 351 " --> pdb=" O GLU h 347 " (cutoff:3.500A) Processing helix chain 'h' and resid 355 through 373 Processing helix chain 'h' and resid 376 through 395 removed outlier: 4.259A pdb=" N ILE h 380 " --> pdb=" O ALA h 376 " (cutoff:3.500A) Processing helix chain 'h' and resid 400 through 407 removed outlier: 3.587A pdb=" N ASN h 404 " --> pdb=" O SER h 400 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 427 removed outlier: 4.355A pdb=" N ASN h 427 " --> pdb=" O SER h 423 " (cutoff:3.500A) Processing helix chain 'h' and resid 432 through 449 Processing helix chain 'h' and resid 453 through 461 Processing helix chain 'h' and resid 462 through 469 Processing helix chain 'h' and resid 470 through 485 removed outlier: 4.021A pdb=" N SER h 485 " --> pdb=" O MET h 481 " (cutoff:3.500A) Processing helix chain 'h' and resid 504 through 519 Processing helix chain 'h' and resid 521 through 536 Processing helix chain 'h' and resid 540 through 544 Processing helix chain 'h' and resid 551 through 560 removed outlier: 3.840A pdb=" N GLY h 556 " --> pdb=" O SER h 552 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL h 557 " --> pdb=" O VAL h 553 " (cutoff:3.500A) Processing helix chain 'h' and resid 563 through 583 Processing helix chain 'h' and resid 585 through 601 Processing helix chain 'h' and resid 604 through 626 Processing helix chain 'h' and resid 635 through 648 Processing helix chain 'h' and resid 656 through 670 removed outlier: 3.949A pdb=" N ALA h 660 " --> pdb=" O ARG h 656 " (cutoff:3.500A) Processing helix chain 'h' and resid 672 through 679 Processing helix chain 'h' and resid 681 through 688 removed outlier: 3.522A pdb=" N LEU h 685 " --> pdb=" O PRO h 681 " (cutoff:3.500A) Processing helix chain 'h' and resid 688 through 703 Processing helix chain 'h' and resid 706 through 725 removed outlier: 3.679A pdb=" N ARG h 712 " --> pdb=" O LYS h 708 " (cutoff:3.500A) Processing helix chain 'h' and resid 744 through 748 removed outlier: 3.776A pdb=" N THR h 748 " --> pdb=" O ARG h 745 " (cutoff:3.500A) Processing helix chain 'h' and resid 753 through 762 Processing helix chain 'h' and resid 766 through 783 removed outlier: 3.513A pdb=" N VAL h 783 " --> pdb=" O LYS h 779 " (cutoff:3.500A) Processing helix chain 'h' and resid 805 through 809 Processing helix chain 'h' and resid 810 through 829 Processing helix chain 'h' and resid 832 through 846 Processing helix chain 'h' and resid 848 through 863 Processing helix chain 'h' and resid 877 through 891 Processing helix chain 'h' and resid 893 through 901 Processing helix chain 'h' and resid 902 through 904 No H-bonds generated for 'chain 'h' and resid 902 through 904' Processing helix chain 'h' and resid 908 through 917 Processing helix chain 'h' and resid 924 through 932 removed outlier: 4.211A pdb=" N ASP h 930 " --> pdb=" O SER h 927 " (cutoff:3.500A) Processing helix chain 'h' and resid 934 through 948 Processing helix chain 'h' and resid 950 through 962 Processing helix chain 'h' and resid 963 through 967 Processing helix chain 'h' and resid 971 through 995 Processing helix chain 'i' and resid 31 through 38 removed outlier: 3.761A pdb=" N SER i 34 " --> pdb=" O ASP i 31 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 51 Processing helix chain 'i' and resid 92 through 96 Processing helix chain 'i' and resid 109 through 117 removed outlier: 3.698A pdb=" N THR i 117 " --> pdb=" O ILE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 147 removed outlier: 4.596A pdb=" N VAL i 147 " --> pdb=" O PHE i 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 154 through 157 Processing helix chain 'i' and resid 158 through 163 removed outlier: 4.096A pdb=" N ARG i 163 " --> pdb=" O LYS i 159 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 171 Processing helix chain 'i' and resid 174 through 176 No H-bonds generated for 'chain 'i' and resid 174 through 176' Processing helix chain 'i' and resid 183 through 192 Processing helix chain 'i' and resid 252 through 256 Processing helix chain 'i' and resid 273 through 291 Processing helix chain 'i' and resid 304 through 320 removed outlier: 3.996A pdb=" N ASP i 317 " --> pdb=" O TYR i 313 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER i 318 " --> pdb=" O GLN i 314 " (cutoff:3.500A) Processing helix chain 'i' and resid 332 through 343 Processing helix chain 'i' and resid 348 through 353 Processing helix chain 'i' and resid 354 through 356 No H-bonds generated for 'chain 'i' and resid 354 through 356' Processing helix chain 'i' and resid 363 through 370 Processing helix chain 'i' and resid 382 through 387 Processing helix chain 'i' and resid 403 through 413 removed outlier: 4.227A pdb=" N HIS i 407 " --> pdb=" O GLY i 403 " (cutoff:3.500A) Processing helix chain 'i' and resid 428 through 433 removed outlier: 3.566A pdb=" N LEU i 433 " --> pdb=" O TYR i 429 " (cutoff:3.500A) Processing helix chain 'i' and resid 434 through 437 Processing helix chain 'i' and resid 453 through 465 Processing helix chain 'i' and resid 474 through 477 removed outlier: 3.707A pdb=" N GLN i 477 " --> pdb=" O GLN i 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 474 through 477' Processing helix chain 'i' and resid 519 through 526 removed outlier: 3.756A pdb=" N SER i 525 " --> pdb=" O GLU i 521 " (cutoff:3.500A) Processing helix chain 'i' and resid 590 through 597 Processing helix chain 'i' and resid 598 through 601 removed outlier: 3.984A pdb=" N HIS i 601 " --> pdb=" O LEU i 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 598 through 601' Processing helix chain 'i' and resid 641 through 652 removed outlier: 4.364A pdb=" N VAL i 645 " --> pdb=" O GLU i 641 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG i 646 " --> pdb=" O MET i 642 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL i 651 " --> pdb=" O LEU i 647 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 52 removed outlier: 3.742A pdb=" N TYR k 50 " --> pdb=" O ASP k 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR k 52 " --> pdb=" O SER k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 60 removed outlier: 4.085A pdb=" N PHE k 60 " --> pdb=" O ARG k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 60' Processing helix chain 'k' and resid 70 through 75 Processing helix chain 'k' and resid 76 through 85 Processing helix chain 'k' and resid 94 through 114 Proline residue: k 101 - end of helix Processing helix chain 'k' and resid 122 through 132 removed outlier: 3.650A pdb=" N LYS k 131 " --> pdb=" O LYS k 127 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS k 132 " --> pdb=" O ASP k 128 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 231 removed outlier: 3.959A pdb=" N ARG k 231 " --> pdb=" O GLU k 227 " (cutoff:3.500A) Processing helix chain 'k' and resid 244 through 257 Processing helix chain 'k' and resid 268 through 282 Processing helix chain 'k' and resid 283 through 286 Processing helix chain 'k' and resid 287 through 294 removed outlier: 3.570A pdb=" N THR k 293 " --> pdb=" O LYS k 289 " (cutoff:3.500A) Processing helix chain 'k' and resid 310 through 314 Processing helix chain 'k' and resid 331 through 339 removed outlier: 3.681A pdb=" N LYS k 339 " --> pdb=" O GLN k 335 " (cutoff:3.500A) Processing helix chain 'k' and resid 359 through 364 removed outlier: 3.564A pdb=" N LYS k 362 " --> pdb=" O VAL k 359 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE k 363 " --> pdb=" O GLY k 360 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU k 364 " --> pdb=" O HIS k 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 359 through 364' Processing helix chain 'k' and resid 394 through 406 Processing helix chain 'k' and resid 416 through 432 removed outlier: 3.634A pdb=" N PHE k 422 " --> pdb=" O LYS k 418 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG k 432 " --> pdb=" O GLU k 428 " (cutoff:3.500A) Processing helix chain 'k' and resid 457 through 469 removed outlier: 3.972A pdb=" N MET k 465 " --> pdb=" O LEU k 461 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN k 467 " --> pdb=" O ARG k 463 " (cutoff:3.500A) Processing helix chain 'k' and resid 494 through 502 removed outlier: 3.825A pdb=" N LEU k 502 " --> pdb=" O ALA k 498 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 529 removed outlier: 3.623A pdb=" N ARG k 529 " --> pdb=" O GLU k 525 " (cutoff:3.500A) Processing helix chain 'k' and resid 530 through 533 Processing helix chain 'k' and resid 580 through 593 removed outlier: 3.811A pdb=" N GLY k 584 " --> pdb=" O ASP k 580 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS k 593 " --> pdb=" O SER k 589 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 58 removed outlier: 3.597A pdb=" N SER m 58 " --> pdb=" O CYS m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 68 removed outlier: 3.578A pdb=" N ARG m 64 " --> pdb=" O MET m 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE m 65 " --> pdb=" O GLU m 61 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET m 66 " --> pdb=" O TYR m 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP m 68 " --> pdb=" O ARG m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 96 Processing helix chain 'm' and resid 97 through 106 removed outlier: 3.851A pdb=" N LEU m 101 " --> pdb=" O ASN m 97 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET m 102 " --> pdb=" O LEU m 98 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA m 103 " --> pdb=" O GLN m 99 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA m 104 " --> pdb=" O GLU m 100 " (cutoff:3.500A) Processing helix chain 'm' and resid 121 through 125 removed outlier: 3.843A pdb=" N HIS m 124 " --> pdb=" O SER m 121 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY m 125 " --> pdb=" O ILE m 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 121 through 125' Processing helix chain 'm' and resid 143 through 148 Processing helix chain 'm' and resid 172 through 186 removed outlier: 3.878A pdb=" N GLU m 176 " --> pdb=" O VAL m 172 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS m 186 " --> pdb=" O THR m 182 " (cutoff:3.500A) Processing helix chain 'm' and resid 187 through 190 removed outlier: 3.629A pdb=" N ALA m 190 " --> pdb=" O ASN m 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 187 through 190' Processing helix chain 'm' and resid 246 through 254 Processing helix chain 'm' and resid 286 through 294 removed outlier: 4.197A pdb=" N HIS m 290 " --> pdb=" O HIS m 286 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU m 294 " --> pdb=" O HIS m 290 " (cutoff:3.500A) Processing helix chain 'm' and resid 348 through 353 removed outlier: 4.140A pdb=" N PHE m 353 " --> pdb=" O CYS m 349 " (cutoff:3.500A) Processing helix chain 'm' and resid 418 through 423 removed outlier: 4.136A pdb=" N PHE m 421 " --> pdb=" O PHE m 418 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET m 422 " --> pdb=" O GLY m 419 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG m 423 " --> pdb=" O GLU m 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 418 through 423' Processing helix chain 'm' and resid 446 through 457 removed outlier: 3.695A pdb=" N ARG m 457 " --> pdb=" O GLU m 453 " (cutoff:3.500A) Processing helix chain 'm' and resid 477 through 482 removed outlier: 3.552A pdb=" N VAL m 482 " --> pdb=" O ALA m 478 " (cutoff:3.500A) Processing helix chain 'm' and resid 487 through 504 removed outlier: 4.084A pdb=" N VAL m 491 " --> pdb=" O THR m 487 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR m 499 " --> pdb=" O GLN m 495 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 502 " --> pdb=" O ILE m 498 " (cutoff:3.500A) Processing helix chain 'm' and resid 528 through 541 removed outlier: 4.016A pdb=" N MET m 532 " --> pdb=" O GLN m 528 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TRP m 533 " --> pdb=" O TYR m 529 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG m 541 " --> pdb=" O GLU m 537 " (cutoff:3.500A) Processing helix chain 'm' and resid 656 through 667 removed outlier: 3.613A pdb=" N ARG m 660 " --> pdb=" O LEU m 656 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE m 661 " --> pdb=" O TRP m 657 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG m 667 " --> pdb=" O THR m 663 " (cutoff:3.500A) Processing helix chain 'm' and resid 672 through 677 Processing helix chain 'j' and resid 3 through 17 Processing helix chain 'j' and resid 21 through 30 removed outlier: 3.962A pdb=" N ALA j 25 " --> pdb=" O ASP j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 35 through 40 Processing helix chain 'j' and resid 42 through 49 removed outlier: 3.641A pdb=" N TYR j 47 " --> pdb=" O GLN j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 70 removed outlier: 3.946A pdb=" N ALA j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA j 59 " --> pdb=" O ARG j 55 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY j 60 " --> pdb=" O THR j 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR j 64 " --> pdb=" O GLY j 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP j 65 " --> pdb=" O ARG j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 87 removed outlier: 3.667A pdb=" N SER j 85 " --> pdb=" O SER j 81 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA j 86 " --> pdb=" O ILE j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 105 Processing helix chain 'j' and resid 107 through 121 removed outlier: 4.327A pdb=" N LYS j 117 " --> pdb=" O GLU j 113 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL j 118 " --> pdb=" O MET j 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 124 through 139 Processing helix chain 'j' and resid 147 through 162 removed outlier: 4.596A pdb=" N GLY j 151 " --> pdb=" O GLY j 147 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU j 152 " --> pdb=" O VAL j 148 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU j 162 " --> pdb=" O GLU j 158 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 185 removed outlier: 4.111A pdb=" N LEU j 179 " --> pdb=" O VAL j 175 " (cutoff:3.500A) Proline residue: j 180 - end of helix Processing helix chain 'j' and resid 191 through 212 Processing helix chain 'j' and resid 246 through 251 Processing helix chain 'j' and resid 254 through 270 Processing helix chain 'j' and resid 287 through 292 Processing helix chain 'j' and resid 303 through 330 Processing helix chain 'j' and resid 350 through 356 Processing helix chain 'j' and resid 368 through 375 Processing helix chain 'j' and resid 389 through 394 removed outlier: 3.507A pdb=" N ASN j 393 " --> pdb=" O ALA j 389 " (cutoff:3.500A) Processing helix chain 'j' and resid 408 through 426 removed outlier: 3.619A pdb=" N ALA j 416 " --> pdb=" O SER j 412 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG j 417 " --> pdb=" O PHE j 413 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU j 418 " --> pdb=" O LYS j 414 " (cutoff:3.500A) Processing helix chain 'j' and resid 426 through 440 Processing helix chain 'j' and resid 445 through 460 Processing helix chain 'j' and resid 461 through 478 removed outlier: 3.757A pdb=" N ALA j 465 " --> pdb=" O GLN j 461 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA j 473 " --> pdb=" O LEU j 469 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA j 474 " --> pdb=" O HIS j 470 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN j 476 " --> pdb=" O LEU j 472 " (cutoff:3.500A) Processing helix chain 'j' and resid 489 through 507 Processing helix chain 'j' and resid 508 through 521 Processing helix chain 'j' and resid 559 through 564 removed outlier: 3.515A pdb=" N TYR j 563 " --> pdb=" O ALA j 559 " (cutoff:3.500A) Processing helix chain 'j' and resid 564 through 578 removed outlier: 4.244A pdb=" N MET j 568 " --> pdb=" O CYS j 564 " (cutoff:3.500A) Processing helix chain 'j' and resid 582 through 592 Processing helix chain 'j' and resid 593 through 595 No H-bonds generated for 'chain 'j' and resid 593 through 595' Processing helix chain 'j' and resid 598 through 615 removed outlier: 4.342A pdb=" N ASN j 602 " --> pdb=" O PRO j 598 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU j 603 " --> pdb=" O ARG j 599 " (cutoff:3.500A) Processing helix chain 'j' and resid 628 through 640 removed outlier: 4.176A pdb=" N THR j 640 " --> pdb=" O ALA j 636 " (cutoff:3.500A) Processing helix chain 'j' and resid 641 through 644 Processing helix chain 'j' and resid 669 through 685 Processing helix chain 'j' and resid 689 through 701 removed outlier: 4.278A pdb=" N VAL j 693 " --> pdb=" O ASN j 689 " (cutoff:3.500A) Processing helix chain 'j' and resid 701 through 710 removed outlier: 3.752A pdb=" N LEU j 705 " --> pdb=" O GLU j 701 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 14 removed outlier: 3.633A pdb=" N THR n 14 " --> pdb=" O LEU n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 46 removed outlier: 5.212A pdb=" N GLU n 40 " --> pdb=" O THR n 36 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS n 41 " --> pdb=" O MET n 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 78 Processing helix chain 'n' and resid 92 through 103 Processing helix chain 'n' and resid 126 through 130 removed outlier: 4.183A pdb=" N SER n 129 " --> pdb=" O LEU n 126 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU n 130 " --> pdb=" O ARG n 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 126 through 130' Processing helix chain 'n' and resid 136 through 140 Processing helix chain 'n' and resid 159 through 164 Processing helix chain 'n' and resid 165 through 167 No H-bonds generated for 'chain 'n' and resid 165 through 167' Processing helix chain 'n' and resid 168 through 174 removed outlier: 3.607A pdb=" N LEU n 172 " --> pdb=" O SER n 168 " (cutoff:3.500A) Processing helix chain 'n' and resid 193 through 197 Processing helix chain 'n' and resid 200 through 205 removed outlier: 3.737A pdb=" N LYS n 203 " --> pdb=" O MET n 200 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU n 204 " --> pdb=" O PHE n 201 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE n 205 " --> pdb=" O GLY n 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 200 through 205' Processing helix chain 'n' and resid 299 through 304 removed outlier: 4.228A pdb=" N ALA n 303 " --> pdb=" O ALA n 299 " (cutoff:3.500A) Processing helix chain 'n' and resid 408 through 420 Processing helix chain 'n' and resid 429 through 433 removed outlier: 3.535A pdb=" N THR n 432 " --> pdb=" O LYS n 429 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE n 433 " --> pdb=" O THR n 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 429 through 433' Processing helix chain 'n' and resid 436 through 439 Processing helix chain 'n' and resid 440 through 447 Processing helix chain 'n' and resid 449 through 455 Processing helix chain 'n' and resid 455 through 467 Processing helix chain 'n' and resid 476 through 480 removed outlier: 3.614A pdb=" N LEU n 479 " --> pdb=" O ALA n 476 " (cutoff:3.500A) Processing helix chain 'n' and resid 481 through 488 Processing helix chain 'n' and resid 493 through 497 removed outlier: 3.557A pdb=" N ALA n 497 " --> pdb=" O SER n 494 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 10 removed outlier: 3.974A pdb=" N ARG o 10 " --> pdb=" O HIS o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 28 Processing helix chain 'o' and resid 30 through 35 Processing helix chain 'o' and resid 41 through 53 removed outlier: 4.194A pdb=" N GLU o 46 " --> pdb=" O LYS o 42 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU o 47 " --> pdb=" O GLY o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 68 through 84 Processing helix chain 'o' and resid 87 through 96 removed outlier: 4.159A pdb=" N ARG o 91 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 99 No H-bonds generated for 'chain 'o' and resid 97 through 99' Processing helix chain 'o' and resid 106 through 124 Processing helix chain 'o' and resid 126 through 140 removed outlier: 3.717A pdb=" N ALA o 134 " --> pdb=" O LEU o 130 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER o 135 " --> pdb=" O GLU o 131 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU o 137 " --> pdb=" O ALA o 133 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN o 138 " --> pdb=" O ALA o 134 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG o 139 " --> pdb=" O SER o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 158 removed outlier: 3.636A pdb=" N CYS o 145 " --> pdb=" O PRO o 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 163 through 174 Processing helix chain 'o' and resid 174 through 188 removed outlier: 3.564A pdb=" N ILE o 182 " --> pdb=" O CYS o 178 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR o 183 " --> pdb=" O CYS o 179 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER o 184 " --> pdb=" O GLN o 180 " (cutoff:3.500A) Processing helix chain 'o' and resid 199 through 224 Proline residue: o 214 - end of helix Processing helix chain 'o' and resid 239 through 249 Processing helix chain 'o' and resid 249 through 257 removed outlier: 4.201A pdb=" N LYS o 255 " --> pdb=" O PRO o 251 " (cutoff:3.500A) Processing helix chain 'o' and resid 277 through 283 Processing helix chain 'o' and resid 283 through 305 Processing helix chain 'o' and resid 321 through 334 removed outlier: 3.538A pdb=" N LEU o 332 " --> pdb=" O GLU o 328 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP o 334 " --> pdb=" O ASN o 330 " (cutoff:3.500A) Processing helix chain 'o' and resid 336 through 341 removed outlier: 3.506A pdb=" N ASN o 340 " --> pdb=" O LEU o 336 " (cutoff:3.500A) Processing helix chain 'o' and resid 341 through 361 Processing helix chain 'o' and resid 369 through 376 Processing helix chain 'o' and resid 377 through 379 No H-bonds generated for 'chain 'o' and resid 377 through 379' Processing helix chain 'o' and resid 382 through 390 Processing sheet with id=AA1, first strand: chain 'q' and resid 45 through 48 Processing sheet with id=AA2, first strand: chain 'q' and resid 111 through 113 Processing sheet with id=AA3, first strand: chain 'q' and resid 202 through 203 Processing sheet with id=AA4, first strand: chain 'q' and resid 237 through 239 removed outlier: 6.346A pdb=" N VAL q 237 " --> pdb=" O VAL q 257 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE q 259 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG q 239 " --> pdb=" O ILE q 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 1159 through 1162 Processing sheet with id=AA6, first strand: chain 'd' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain 'd' and resid 821 through 824 removed outlier: 7.479A pdb=" N ARG d 889 " --> pdb=" O PRO d 885 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 835 through 836 removed outlier: 6.187A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS d 907 " --> pdb=" O ILE d 956 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 835 through 836 removed outlier: 6.187A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS d 907 " --> pdb=" O ILE d 956 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 42 through 43 Processing sheet with id=AB2, first strand: chain 'e' and resid 961 through 963 Processing sheet with id=AB3, first strand: chain 'f' and resid 62 through 64 removed outlier: 6.600A pdb=" N ILE f 3 " --> pdb=" O ILE f 124 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE f 126 " --> pdb=" O ILE f 3 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU f 5 " --> pdb=" O ILE f 126 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE f 128 " --> pdb=" O LEU f 5 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU f 7 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP f 130 " --> pdb=" O LEU f 7 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA f 123 " --> pdb=" O ARG f 167 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE f 169 " --> pdb=" O ALA f 123 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE f 125 " --> pdb=" O PHE f 169 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU f 171 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR f 127 " --> pdb=" O LEU f 171 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU f 173 " --> pdb=" O THR f 127 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR f 129 " --> pdb=" O LEU f 173 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR f 208 " --> pdb=" O LEU f 168 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA f 170 " --> pdb=" O TYR f 208 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL f 210 " --> pdb=" O ALA f 170 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL f 172 " --> pdb=" O VAL f 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 134 through 135 removed outlier: 3.667A pdb=" N LEU f 134 " --> pdb=" O GLN f 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 263 through 269 removed outlier: 3.738A pdb=" N GLN f 349 " --> pdb=" O SER f 310 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY f 366 " --> pdb=" O VAL f 350 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL f 352 " --> pdb=" O PRO f 364 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP f 325 " --> pdb=" O VAL f 381 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'g' and resid 803 through 804 Processing sheet with id=AB8, first strand: chain 'g' and resid 819 through 822 removed outlier: 5.995A pdb=" N ILE g 819 " --> pdb=" O LYS g 929 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU g 931 " --> pdb=" O ILE g 819 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL g 821 " --> pdb=" O LEU g 931 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 819 through 822 removed outlier: 5.995A pdb=" N ILE g 819 " --> pdb=" O LYS g 929 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU g 931 " --> pdb=" O ILE g 819 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL g 821 " --> pdb=" O LEU g 931 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 62 through 63 Processing sheet with id=AC2, first strand: chain 'h' and resid 212 through 214 Processing sheet with id=AC3, first strand: chain 'i' and resid 194 through 196 removed outlier: 6.511A pdb=" N VAL i 123 " --> pdb=" O GLN i 195 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE i 99 " --> pdb=" O TYR i 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL i 98 " --> pdb=" O THR i 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR i 22 " --> pdb=" O PHE i 19 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS i 2 " --> pdb=" O LYS i 18 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU i 503 " --> pdb=" O CYS i 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'i' and resid 68 through 71 Processing sheet with id=AC5, first strand: chain 'i' and resid 83 through 84 Processing sheet with id=AC6, first strand: chain 'i' and resid 203 through 205 removed outlier: 3.674A pdb=" N VAL i 209 " --> pdb=" O LEU i 205 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR i 499 " --> pdb=" O VAL i 469 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS i 471 " --> pdb=" O TYR i 499 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'i' and resid 373 through 376 removed outlier: 6.059A pdb=" N LEU i 326 " --> pdb=" O LYS i 374 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR i 376 " --> pdb=" O LEU i 326 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE i 328 " --> pdb=" O TYR i 376 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR i 327 " --> pdb=" O PHE i 394 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU i 296 " --> pdb=" O ILE i 421 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL i 420 " --> pdb=" O ILE i 444 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 528 through 530 removed outlier: 3.603A pdb=" N LEU i 537 " --> pdb=" O MET i 529 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU k 492 " --> pdb=" O PRO k 453 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY k 455 " --> pdb=" O LEU k 492 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS i 515 " --> pdb=" O HIS i 551 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LEU i 553 " --> pdb=" O LYS i 515 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU i 517 " --> pdb=" O LEU i 553 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 586 through 587 Processing sheet with id=AD1, first strand: chain 'i' and resid 606 through 609 removed outlier: 3.733A pdb=" N LYS i 607 " --> pdb=" O LEU i 618 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU i 618 " --> pdb=" O LYS i 607 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE i 635 " --> pdb=" O ARG k 510 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'k' and resid 133 through 136 removed outlier: 5.913A pdb=" N ILE k 90 " --> pdb=" O VAL k 134 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL k 136 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET k 92 " --> pdb=" O VAL k 136 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR k 91 " --> pdb=" O ASP k 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL k 64 " --> pdb=" O TYR k 91 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR k 93 " --> pdb=" O VAL k 64 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN k 28 " --> pdb=" O CYS k 63 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ILE k 65 " --> pdb=" O ASN k 28 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET k 30 " --> pdb=" O ILE k 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS k 19 " --> pdb=" O LEU k 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'k' and resid 148 through 152 removed outlier: 6.761A pdb=" N SER k 172 " --> pdb=" O LEU k 199 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE k 201 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL k 174 " --> pdb=" O ILE k 201 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN k 203 " --> pdb=" O VAL k 174 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU k 412 " --> pdb=" O TYR k 436 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 235 through 238 removed outlier: 6.374A pdb=" N VAL k 235 " --> pdb=" O VAL k 321 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA k 323 " --> pdb=" O VAL k 235 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE k 237 " --> pdb=" O ALA k 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'k' and resid 514 through 517 removed outlier: 3.562A pdb=" N LEU k 572 " --> pdb=" O VAL k 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS k 570 " --> pdb=" O LEU k 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'm' and resid 334 through 336 4772 hydrogen bonds defined for protein. 13866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 33.00 Time building geometry restraints manager: 24.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 26087 1.34 - 1.46: 17187 1.46 - 1.59: 35673 1.59 - 1.71: 1 1.71 - 1.84: 594 Bond restraints: 79542 Sorted by residual: bond pdb=" C VAL q 189 " pdb=" N PRO q 190 " ideal model delta sigma weight residual 1.328 1.363 -0.035 1.26e-02 6.30e+03 7.76e+00 bond pdb=" CB THR p 501 " pdb=" CG2 THR p 501 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.90e+00 bond pdb=" N GLU q 192 " pdb=" CA GLU q 192 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.26e-02 6.30e+03 5.98e+00 bond pdb=" CB VAL e 693 " pdb=" CG2 VAL e 693 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.46e+00 bond pdb=" C PRO e 365 " pdb=" N PRO e 366 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.51e-02 4.39e+03 5.44e+00 ... (remaining 79537 not shown) Histogram of bond angle deviations from ideal: 91.18 - 100.03: 41 100.03 - 108.87: 4625 108.87 - 117.72: 55886 117.72 - 126.57: 46952 126.57 - 135.41: 1027 Bond angle restraints: 108531 Sorted by residual: angle pdb=" CB MET d 701 " pdb=" CG MET d 701 " pdb=" SD MET d 701 " ideal model delta sigma weight residual 112.70 130.02 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" CB LYS i 600 " pdb=" CG LYS i 600 " pdb=" CD LYS i 600 " ideal model delta sigma weight residual 111.30 122.80 -11.50 2.30e+00 1.89e-01 2.50e+01 angle pdb=" CA LEU e 151 " pdb=" CB LEU e 151 " pdb=" CG LEU e 151 " ideal model delta sigma weight residual 116.30 132.91 -16.61 3.50e+00 8.16e-02 2.25e+01 angle pdb=" C LEU j 35 " pdb=" N TYR j 36 " pdb=" CA TYR j 36 " ideal model delta sigma weight residual 119.83 125.06 -5.23 1.11e+00 8.12e-01 2.22e+01 angle pdb=" CA GLN k 376 " pdb=" CB GLN k 376 " pdb=" CG GLN k 376 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 ... (remaining 108526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 43189 17.98 - 35.96: 3792 35.96 - 53.94: 856 53.94 - 71.92: 210 71.92 - 89.90: 92 Dihedral angle restraints: 48139 sinusoidal: 15666 harmonic: 32473 Sorted by residual: dihedral pdb=" CB CYS g 638 " pdb=" SG CYS g 638 " pdb=" SG CYS g 778 " pdb=" CB CYS g 778 " ideal model delta sinusoidal sigma weight residual 93.00 146.48 -53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA ASN q 264 " pdb=" C ASN q 264 " pdb=" N TYR q 265 " pdb=" CA TYR q 265 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TYR a2168 " pdb=" C TYR a2168 " pdb=" N GLY a2169 " pdb=" CA GLY a2169 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 48136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 12011 0.086 - 0.171: 1097 0.171 - 0.257: 43 0.257 - 0.343: 8 0.343 - 0.429: 4 Chirality restraints: 13163 Sorted by residual: chirality pdb=" CG LEU a1173 " pdb=" CB LEU a1173 " pdb=" CD1 LEU a1173 " pdb=" CD2 LEU a1173 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CG LEU d 548 " pdb=" CB LEU d 548 " pdb=" CD1 LEU d 548 " pdb=" CD2 LEU d 548 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB VAL a2189 " pdb=" CA VAL a2189 " pdb=" CG1 VAL a2189 " pdb=" CG2 VAL a2189 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 13160 not shown) Planarity restraints: 14182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP e 225 " -0.042 2.00e-02 2.50e+03 3.53e-02 3.12e+01 pdb=" CG TRP e 225 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP e 225 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP e 225 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP e 225 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP e 225 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP e 225 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 225 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 225 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP e 225 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO h 122 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO h 123 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO h 123 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO h 123 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER d 502 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C SER d 502 " 0.060 2.00e-02 2.50e+03 pdb=" O SER d 502 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE d 503 " -0.021 2.00e-02 2.50e+03 ... (remaining 14179 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 503 2.59 - 3.17: 65479 3.17 - 3.75: 128833 3.75 - 4.32: 163279 4.32 - 4.90: 273138 Nonbonded interactions: 631232 Sorted by model distance: nonbonded pdb=" OD2 ASP k 178 " pdb="ZN ZN k1001 " model vdw 2.017 2.230 nonbonded pdb=" OD1 ASN q 117 " pdb="MN MN q1002 " model vdw 2.130 2.320 nonbonded pdb=" OD2 ASP q 85 " pdb="MN MN q1001 " model vdw 2.142 2.320 nonbonded pdb=" OD2 ASP e 896 " pdb=" OG1 THR e 898 " model vdw 2.203 2.440 nonbonded pdb=" O PHE a1664 " pdb=" OG SER a1668 " model vdw 2.204 2.440 ... (remaining 631227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 23.390 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 169.620 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.240 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3085 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 : 0.005 0.087 79542 Z= 0.325 Angle : 0.800 17.319 108531 Z= 0.416 Chirality : 0.049 0.429 13163 Planarity : 0.005 0.104 14182 Dihedral : 15.580 89.905 26894 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 0.10 % Allowed : 15.17 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 0.73 (0.08), residues: 10951 helix: 1.51 (0.07), residues: 6412 sheet: -0.36 (0.24), residues: 460 loop : -1.07 (0.10), residues: 4079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP e 225 HIS 0.017 0.001 HIS p 520 PHE 0.041 0.002 PHE b 566 TYR 0.025 0.002 TYR p 169 ARG 0.017 0.001 ARG a1126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1055 time to evaluate : 6.813 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: 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: symmetry clash revert: symmetry clash REVERT: q 65 LEU cc_start: 0.5277 (tp) cc_final: 0.3914 (tp) REVERT: a 1131 MET cc_start: -0.4138 (tpp) cc_final: -0.5266 (mtp) REVERT: a 1484 LEU cc_start: 0.4487 (mt) cc_final: 0.3813 (mm) REVERT: a 1996 VAL cc_start: 0.7422 (p) cc_final: 0.6929 (m) REVERT: a 2121 PHE cc_start: 0.2682 (m-80) cc_final: 0.2473 (m-80) REVERT: b 26 MET cc_start: -0.3415 (tpt) cc_final: -0.3627 (tpt) REVERT: b 205 ARG cc_start: 0.8406 (tmt-80) cc_final: 0.8008 (tpm170) REVERT: b 415 MET cc_start: 0.0432 (mtt) cc_final: 0.0028 (mtp) REVERT: b 596 ILE cc_start: 0.3231 (mt) cc_final: 0.3030 (mt) REVERT: b 810 LEU cc_start: 0.7230 (mt) cc_final: 0.6561 (mt) REVERT: b 941 ILE cc_start: 0.9272 (mt) cc_final: 0.8981 (mm) REVERT: b 945 ILE cc_start: 0.8086 (mt) cc_final: 0.7739 (mm) REVERT: b 1014 LEU cc_start: 0.7287 (tp) cc_final: 0.6836 (tp) REVERT: b 1061 LEU cc_start: 0.8958 (tp) cc_final: 0.8755 (tp) REVERT: b 1107 LEU cc_start: 0.8531 (mt) cc_final: 0.8080 (mm) REVERT: b 1150 LEU cc_start: 0.6293 (mt) cc_final: 0.5580 (mt) REVERT: b 1194 ILE cc_start: 0.7894 (mt) cc_final: 0.7620 (mm) REVERT: b 1197 ILE cc_start: 0.7277 (mt) cc_final: 0.6981 (mt) REVERT: d 235 ASN cc_start: 0.8644 (m-40) cc_final: 0.8040 (p0) REVERT: d 701 MET cc_start: 0.4552 (mmm) cc_final: 0.4030 (mmm) REVERT: d 865 VAL cc_start: 0.6196 (t) cc_final: 0.5952 (t) REVERT: e 181 MET cc_start: 0.2352 (mmp) cc_final: 0.1432 (mmt) REVERT: f 363 HIS cc_start: 0.6277 (m90) cc_final: 0.6013 (m90) REVERT: g 232 ILE cc_start: 0.4328 (mt) cc_final: 0.4092 (mt) REVERT: g 318 LEU cc_start: 0.5945 (mt) cc_final: 0.5145 (tp) REVERT: h 130 MET cc_start: 0.0415 (pmm) cc_final: -0.1195 (ptt) REVERT: h 174 MET cc_start: 0.3013 (mmm) cc_final: 0.1744 (mmm) REVERT: h 350 LEU cc_start: 0.7360 (mp) cc_final: 0.6953 (mp) REVERT: h 535 MET cc_start: 0.1513 (pmm) cc_final: 0.1217 (pmm) REVERT: i 284 ASN cc_start: 0.8516 (m110) cc_final: 0.8131 (m110) REVERT: k 299 MET cc_start: 0.4332 (pmm) cc_final: 0.3896 (ppp) REVERT: k 372 MET cc_start: -0.2608 (tmm) cc_final: -0.5226 (ptt) REVERT: k 437 MET cc_start: 0.6087 (mmm) cc_final: 0.5753 (mmm) REVERT: k 465 MET cc_start: -0.6545 (pmm) cc_final: -0.7044 (ptt) outliers start: 7 outliers final: 0 residues processed: 1060 average time/residue: 0.7604 time to fit residues: 1399.7929 Evaluate side-chains 674 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 933 optimal weight: 0.0470 chunk 837 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 564 optimal weight: 20.0000 chunk 447 optimal weight: 3.9990 chunk 866 optimal weight: 8.9990 chunk 335 optimal weight: 4.9990 chunk 526 optimal weight: 4.9990 chunk 644 optimal weight: 0.7980 chunk 1003 optimal weight: 9.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 230 ASN ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 383 ASN ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 288 GLN a1082 HIS ** a1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1893 HIS b 206 ASN b 217 ASN b 413 GLN ** b 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 851 ASN b 895 HIS b 934 GLN b1187 HIS d 54 GLN d 441 ASN d 468 HIS d 859 ASN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 480 HIS e 989 HIS ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 291 ASN ** g 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 579 GLN g 715 HIS h 176 GLN h 588 HIS h 892 ASN ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 980 GLN ** i 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 627 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3622 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 79542 Z= 0.282 Angle : 0.708 12.753 108531 Z= 0.357 Chirality : 0.044 0.323 13163 Planarity : 0.005 0.073 14182 Dihedral : 4.239 55.683 11625 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.74 % Allowed : 17.24 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 0.56 (0.08), residues: 10951 helix: 1.29 (0.06), residues: 6509 sheet: -0.50 (0.24), residues: 476 loop : -1.03 (0.10), residues: 3966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP r1037 HIS 0.014 0.001 HIS a1893 PHE 0.034 0.002 PHE a1510 TYR 0.032 0.002 TYR h 931 ARG 0.022 0.001 ARG e 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 781 time to evaluate : 6.693 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: 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: 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 65 LEU cc_start: 0.6134 (tp) cc_final: 0.5873 (tp) REVERT: a 1107 LEU cc_start: -0.3973 (OUTLIER) cc_final: -0.4190 (pp) REVERT: a 1131 MET cc_start: -0.4226 (tpp) cc_final: -0.4541 (ptm) REVERT: a 1207 ASP cc_start: -0.0713 (OUTLIER) cc_final: -0.1844 (p0) REVERT: a 1970 ASN cc_start: 0.1633 (OUTLIER) cc_final: 0.0445 (t0) REVERT: b 205 ARG cc_start: 0.8401 (tmt-80) cc_final: 0.8018 (tpp-160) REVERT: b 505 MET cc_start: -0.0636 (ptp) cc_final: -0.0926 (ptp) REVERT: b 596 ILE cc_start: 0.2613 (mt) cc_final: 0.1939 (mt) REVERT: b 727 TRP cc_start: 0.7404 (m100) cc_final: 0.7119 (m100) REVERT: b 941 ILE cc_start: 0.9514 (mt) cc_final: 0.9239 (mm) REVERT: b 1194 ILE cc_start: 0.9162 (mt) cc_final: 0.8890 (mt) REVERT: d 235 ASN cc_start: 0.8809 (m-40) cc_final: 0.8225 (p0) REVERT: d 509 PHE cc_start: 0.8417 (m-80) cc_final: 0.8064 (m-10) REVERT: d 561 MET cc_start: 0.7861 (tpp) cc_final: 0.7483 (tpp) REVERT: e 181 MET cc_start: 0.1911 (mmp) cc_final: 0.1294 (mmt) REVERT: e 406 LEU cc_start: 0.8653 (mm) cc_final: 0.8396 (mt) REVERT: e 415 MET cc_start: 0.1894 (OUTLIER) cc_final: 0.1533 (mmp) REVERT: e 549 LEU cc_start: 0.2216 (OUTLIER) cc_final: 0.1883 (mt) REVERT: e 578 LEU cc_start: 0.6502 (mt) cc_final: 0.6146 (mt) REVERT: e 614 LEU cc_start: 0.6736 (mt) cc_final: 0.6439 (mt) REVERT: f 301 ARG cc_start: -0.1315 (OUTLIER) cc_final: -0.4277 (mmp-170) REVERT: f 433 MET cc_start: 0.1909 (ptp) cc_final: 0.1642 (ptp) REVERT: g 74 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8083 (m) REVERT: g 78 PHE cc_start: 0.7692 (t80) cc_final: 0.7467 (t80) REVERT: g 79 LEU cc_start: 0.8000 (mt) cc_final: 0.7647 (mt) REVERT: g 627 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5666 (tp) REVERT: h 130 MET cc_start: 0.0671 (pmm) cc_final: -0.0875 (ptt) REVERT: h 225 MET cc_start: 0.7615 (mmt) cc_final: 0.7364 (mmp) REVERT: h 263 GLN cc_start: 0.7438 (mt0) cc_final: 0.7234 (pt0) REVERT: h 609 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7182 (tm-30) REVERT: h 667 MET cc_start: -0.2194 (tpp) cc_final: -0.2704 (tmm) REVERT: h 937 ILE cc_start: 0.6014 (mm) cc_final: 0.5594 (mt) REVERT: h 941 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5540 (tp) REVERT: i 137 MET cc_start: -0.0036 (mtt) cc_final: -0.1014 (mtt) REVERT: i 601 HIS cc_start: -0.1113 (OUTLIER) cc_final: -0.1597 (t-90) REVERT: i 650 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6574 (tp) REVERT: k 299 MET cc_start: 0.4286 (pmm) cc_final: 0.3902 (ppp) REVERT: k 350 MET cc_start: 0.0353 (mtt) cc_final: -0.0338 (tpt) REVERT: k 372 MET cc_start: -0.2534 (tmm) cc_final: -0.5348 (ptt) REVERT: k 465 MET cc_start: -0.7286 (pmm) cc_final: -0.7583 (ptt) outliers start: 193 outliers final: 71 residues processed: 936 average time/residue: 0.6925 time to fit residues: 1138.3239 Evaluate side-chains 735 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 653 time to evaluate : 6.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 79 LEU Chi-restraints excluded: chain p residue 464 SER Chi-restraints excluded: chain p residue 487 LEU Chi-restraints excluded: chain q residue 21 LYS Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 55 CYS Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 234 LEU Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1207 ASP Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1469 SER Chi-restraints excluded: chain a residue 1551 VAL Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1848 ASP Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2043 THR Chi-restraints excluded: chain a residue 2094 SER Chi-restraints excluded: chain b residue 154 SER Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 457 SER Chi-restraints excluded: chain b residue 793 LEU Chi-restraints excluded: chain b residue 800 LEU Chi-restraints excluded: chain b residue 823 VAL Chi-restraints excluded: chain b residue 895 HIS Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1040 ASP Chi-restraints excluded: chain b residue 1079 LEU Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain d residue 231 GLN Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 653 LEU Chi-restraints excluded: chain d residue 690 SER Chi-restraints excluded: chain d residue 694 SER Chi-restraints excluded: chain d residue 883 ARG Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 549 LEU Chi-restraints excluded: chain e residue 574 PHE Chi-restraints excluded: chain e residue 575 LEU Chi-restraints excluded: chain e residue 627 SER Chi-restraints excluded: chain e residue 673 LEU Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 856 LEU Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 301 ARG Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 177 CYS Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 231 VAL Chi-restraints excluded: chain g residue 605 THR Chi-restraints excluded: chain g residue 627 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 850 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 176 GLN Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 608 ARG Chi-restraints excluded: chain h residue 788 VAL Chi-restraints excluded: chain h residue 848 GLN Chi-restraints excluded: chain h residue 862 VAL Chi-restraints excluded: chain h residue 941 LEU Chi-restraints excluded: chain h residue 972 GLU Chi-restraints excluded: chain i residue 195 GLN Chi-restraints excluded: chain i residue 281 PHE Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain i residue 643 LEU Chi-restraints excluded: chain i residue 650 LEU Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 518 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 557 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 835 optimal weight: 10.0000 chunk 683 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 1005 optimal weight: 50.0000 chunk 1085 optimal weight: 20.0000 chunk 895 optimal weight: 30.0000 chunk 996 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 806 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 340 HIS ** p 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 61 GLN ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 288 GLN a1082 HIS a1168 HIS a1242 GLN ** a1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1889 HIS a1893 HIS a1927 HIS a1951 HIS a2113 ASN a2143 ASN b 27 GLN b 616 ASN b 747 ASN ** b 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 895 HIS b1003 GLN b1130 GLN b1187 HIS d 58 GLN d 254 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 633 GLN ** d 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 859 ASN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 770 GLN e 894 HIS e 953 HIS ** g 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 349 GLN ** g 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 570 HIS ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 673 GLN g 702 ASN ** g 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 837 HIS h 127 HIS ** h 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 294 HIS ** h 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 407 HIS ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 GLN k 165 GLN ** k 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 376 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4349 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 79542 Z= 0.448 Angle : 0.938 26.398 108531 Z= 0.473 Chirality : 0.051 0.433 13163 Planarity : 0.007 0.158 14182 Dihedral : 5.074 64.955 11625 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 4.91 % Allowed : 17.71 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.18 % 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: -0.27 (0.08), residues: 10951 helix: 0.56 (0.06), residues: 6493 sheet: -0.86 (0.23), residues: 458 loop : -1.23 (0.10), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP e 831 HIS 0.044 0.003 HIS b 895 PHE 0.050 0.004 PHE g 57 TYR 0.092 0.003 TYR h 928 ARG 0.019 0.001 ARG e 951 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 713 time to evaluate : 6.764 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: 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: p 469 LEU cc_start: 0.2250 (OUTLIER) cc_final: 0.2023 (tp) REVERT: q 83 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5433 (mpp) REVERT: q 277 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7021 (tp30) REVERT: a 1131 MET cc_start: -0.4217 (tpp) cc_final: -0.4537 (ptt) REVERT: a 1970 ASN cc_start: 0.2162 (OUTLIER) cc_final: 0.1509 (t0) REVERT: a 2184 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (pp) REVERT: b 627 ILE cc_start: 0.5218 (OUTLIER) cc_final: 0.4835 (mt) REVERT: b 628 PHE cc_start: 0.5327 (OUTLIER) cc_final: 0.4633 (m-10) REVERT: b 779 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9054 (p) REVERT: b 1101 MET cc_start: 0.8410 (mmm) cc_final: 0.8157 (mmm) REVERT: b 1132 CYS cc_start: 0.7265 (t) cc_final: 0.6912 (t) REVERT: b 1144 ASP cc_start: 0.5694 (OUTLIER) cc_final: 0.5425 (m-30) REVERT: d 386 GLU cc_start: 0.2809 (OUTLIER) cc_final: 0.2370 (pm20) REVERT: d 701 MET cc_start: 0.3469 (mmm) cc_final: 0.3265 (mmt) REVERT: e 181 MET cc_start: 0.2110 (mmp) cc_final: 0.1510 (mmt) REVERT: e 415 MET cc_start: 0.3148 (OUTLIER) cc_final: 0.2750 (mmm) REVERT: e 438 LEU cc_start: 0.5099 (pp) cc_final: 0.4854 (mt) REVERT: e 549 LEU cc_start: 0.3863 (OUTLIER) cc_final: 0.3376 (mt) REVERT: e 856 LEU cc_start: 0.3350 (OUTLIER) cc_final: 0.3030 (pp) REVERT: e 857 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.4049 (mt) REVERT: e 997 ASP cc_start: 0.0940 (OUTLIER) cc_final: 0.0415 (p0) REVERT: f 33 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5079 (mm-30) REVERT: f 127 THR cc_start: 0.3809 (OUTLIER) cc_final: 0.3594 (t) REVERT: f 215 MET cc_start: 0.3908 (mmt) cc_final: 0.3450 (mmm) REVERT: f 301 ARG cc_start: -0.0813 (OUTLIER) cc_final: -0.4276 (mmm160) REVERT: g 230 MET cc_start: 0.9228 (mmm) cc_final: 0.9021 (tpp) REVERT: g 257 LEU cc_start: 0.3553 (OUTLIER) cc_final: 0.3050 (mt) REVERT: g 544 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6268 (pt0) REVERT: g 627 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6794 (tt) REVERT: g 637 THR cc_start: 0.5838 (OUTLIER) cc_final: 0.5483 (p) REVERT: h 130 MET cc_start: 0.1035 (pmm) cc_final: -0.0431 (ptt) REVERT: h 344 ILE cc_start: 0.7103 (mt) cc_final: 0.6765 (tt) REVERT: h 609 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6927 (tm-30) REVERT: h 837 ILE cc_start: 0.6561 (mm) cc_final: 0.6200 (mm) REVERT: h 838 ILE cc_start: 0.7872 (mt) cc_final: 0.7573 (mp) REVERT: h 842 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6522 (mt) REVERT: h 885 ILE cc_start: 0.7243 (mt) cc_final: 0.6502 (mt) REVERT: h 925 MET cc_start: 0.8349 (mtm) cc_final: 0.8119 (mtm) REVERT: i 108 MET cc_start: 0.1250 (OUTLIER) cc_final: -0.0123 (mmp) REVERT: i 240 SER cc_start: 0.7487 (m) cc_final: 0.7111 (t) REVERT: i 281 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6147 (t80) REVERT: i 441 MET cc_start: 0.1383 (tpt) cc_final: 0.0971 (tpp) REVERT: i 486 MET cc_start: 0.8185 (tpt) cc_final: 0.7863 (ttt) REVERT: i 601 HIS cc_start: -0.0945 (OUTLIER) cc_final: -0.2056 (t-90) REVERT: i 642 MET cc_start: 0.8497 (mmp) cc_final: 0.8103 (pmm) REVERT: i 650 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6725 (pp) REVERT: k 299 MET cc_start: 0.4384 (pmm) cc_final: 0.3959 (ppp) REVERT: k 350 MET cc_start: 0.0103 (mtt) cc_final: -0.0226 (tpt) REVERT: k 372 MET cc_start: -0.2689 (tmm) cc_final: -0.5281 (ptt) REVERT: k 420 MET cc_start: -0.4074 (mtt) cc_final: -0.4464 (mtt) REVERT: k 518 HIS cc_start: 0.9425 (OUTLIER) cc_final: 0.8835 (t70) REVERT: m 689 LEU cc_start: -0.2000 (mt) cc_final: -0.2245 (mp) outliers start: 346 outliers final: 139 residues processed: 1004 average time/residue: 0.6946 time to fit residues: 1242.3125 Evaluate side-chains 769 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 603 time to evaluate : 6.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 79 LEU Chi-restraints excluded: chain p residue 142 THR Chi-restraints excluded: chain p residue 284 VAL Chi-restraints excluded: chain p residue 469 LEU Chi-restraints excluded: chain p residue 500 THR Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 55 CYS Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 93 SER Chi-restraints excluded: chain q residue 98 THR Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain q residue 170 LEU Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 178 ASP Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 230 HIS Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 287 LEU Chi-restraints excluded: chain q residue 289 PHE Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain r residue 1040 ASN Chi-restraints excluded: chain r residue 1045 ILE Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1615 SER Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1795 LEU Chi-restraints excluded: chain a residue 1848 ASP Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2092 MET Chi-restraints excluded: chain a residue 2094 SER Chi-restraints excluded: chain a residue 2146 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain a residue 2184 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 154 SER Chi-restraints excluded: chain b residue 335 VAL Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 457 SER Chi-restraints excluded: chain b residue 540 VAL Chi-restraints excluded: chain b residue 554 ILE Chi-restraints excluded: chain b residue 583 GLU Chi-restraints excluded: chain b residue 592 LEU Chi-restraints excluded: chain b residue 602 SER Chi-restraints excluded: chain b residue 624 ILE Chi-restraints excluded: chain b residue 627 ILE Chi-restraints excluded: chain b residue 628 PHE Chi-restraints excluded: chain b residue 646 THR Chi-restraints excluded: chain b residue 651 VAL Chi-restraints excluded: chain b residue 655 ILE Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 779 THR Chi-restraints excluded: chain b residue 833 VAL Chi-restraints excluded: chain b residue 859 ILE Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1040 ASP Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1144 ASP Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 386 GLU Chi-restraints excluded: chain d residue 467 LEU Chi-restraints excluded: chain d residue 501 ASP Chi-restraints excluded: chain d residue 522 VAL Chi-restraints excluded: chain d residue 649 LEU Chi-restraints excluded: chain d residue 702 GLU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 845 LEU Chi-restraints excluded: chain d residue 876 HIS Chi-restraints excluded: chain d residue 883 ARG Chi-restraints excluded: chain d residue 901 THR Chi-restraints excluded: chain d residue 946 ILE Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 473 PHE Chi-restraints excluded: chain e residue 549 LEU Chi-restraints excluded: chain e residue 575 LEU Chi-restraints excluded: chain e residue 613 LEU Chi-restraints excluded: chain e residue 627 SER Chi-restraints excluded: chain e residue 701 ASN Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 799 TRP Chi-restraints excluded: chain e residue 845 LEU Chi-restraints excluded: chain e residue 856 LEU Chi-restraints excluded: chain e residue 857 LEU Chi-restraints excluded: chain e residue 862 LYS Chi-restraints excluded: chain e residue 877 LEU Chi-restraints excluded: chain e residue 897 THR Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain e residue 997 ASP Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 145 HIS Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 267 LEU Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 301 ARG Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 385 ASN Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 151 ASP Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 321 THR Chi-restraints excluded: chain g residue 414 ASN Chi-restraints excluded: chain g residue 462 VAL Chi-restraints excluded: chain g residue 543 LYS Chi-restraints excluded: chain g residue 544 GLU Chi-restraints excluded: chain g residue 605 THR Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 625 ILE Chi-restraints excluded: chain g residue 627 LEU Chi-restraints excluded: chain g residue 635 ILE Chi-restraints excluded: chain g residue 637 THR Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 700 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 924 THR Chi-restraints excluded: chain h residue 105 VAL Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain h residue 424 ARG Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 608 ARG Chi-restraints excluded: chain h residue 676 LEU Chi-restraints excluded: chain h residue 788 VAL Chi-restraints excluded: chain h residue 818 VAL Chi-restraints excluded: chain h residue 822 VAL Chi-restraints excluded: chain h residue 828 ILE Chi-restraints excluded: chain h residue 842 ILE Chi-restraints excluded: chain h residue 848 GLN Chi-restraints excluded: chain h residue 853 LEU Chi-restraints excluded: chain h residue 897 VAL Chi-restraints excluded: chain h residue 921 SER Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 941 LEU Chi-restraints excluded: chain h residue 972 GLU Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 195 GLN Chi-restraints excluded: chain i residue 224 ASN Chi-restraints excluded: chain i residue 281 PHE Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain i residue 643 LEU Chi-restraints excluded: chain i residue 650 LEU Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 518 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 993 optimal weight: 9.9990 chunk 755 optimal weight: 5.9990 chunk 521 optimal weight: 0.6980 chunk 111 optimal weight: 30.0000 chunk 479 optimal weight: 8.9990 chunk 675 optimal weight: 0.7980 chunk 1008 optimal weight: 50.0000 chunk 1068 optimal weight: 5.9990 chunk 527 optimal weight: 0.6980 chunk 956 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 444 ASN ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN ** q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2087 ASN a2160 HIS ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 622 GLN ** b 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1130 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 818 HIS d 859 ASN d 864 GLN d 876 HIS e 445 HIS e 452 HIS e 662 HIS ** e 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 ASN f 70 HIS ** f 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 586 GLN ** g 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 GLN g 355 ASN g 369 ASN g 516 GLN ** g 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 127 HIS h 328 GLN ** h 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 404 ASN ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 922 HIS ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 615 HIS k 13 GLN ** k 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 376 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4239 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 79542 Z= 0.209 Angle : 0.654 14.928 108531 Z= 0.321 Chirality : 0.042 0.267 13163 Planarity : 0.004 0.067 14182 Dihedral : 4.366 58.983 11625 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 2.75 % Allowed : 20.48 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 0.42 (0.08), residues: 10951 helix: 1.16 (0.06), residues: 6523 sheet: -0.62 (0.23), residues: 464 loop : -1.04 (0.10), residues: 3964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP d 679 HIS 0.016 0.001 HIS a1893 PHE 0.032 0.002 PHE h 986 TYR 0.044 0.002 TYR q 145 ARG 0.036 0.001 ARG k 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 634 time to evaluate : 6.726 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: 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: p 397 ILE cc_start: 0.5249 (OUTLIER) cc_final: 0.4946 (tt) REVERT: a 1131 MET cc_start: -0.4272 (tpp) cc_final: -0.4476 (ptm) REVERT: a 1162 MET cc_start: -0.2458 (OUTLIER) cc_final: -0.3245 (ppp) REVERT: a 1223 MET cc_start: 0.3463 (tpp) cc_final: 0.3220 (mmt) REVERT: a 1970 ASN cc_start: 0.2365 (OUTLIER) cc_final: 0.1657 (t0) REVERT: a 2047 MET cc_start: 0.0994 (pmm) cc_final: 0.0157 (pmm) REVERT: a 2184 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8855 (pp) REVERT: b 348 MET cc_start: 0.7927 (mmm) cc_final: 0.7708 (mmm) REVERT: b 479 MET cc_start: 0.0053 (OUTLIER) cc_final: -0.0460 (tmm) REVERT: b 737 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (p0) REVERT: b 1128 ILE cc_start: 0.9432 (mt) cc_final: 0.8821 (mt) REVERT: b 1199 MET cc_start: 0.8970 (tmm) cc_final: 0.8651 (tmm) REVERT: d 386 GLU cc_start: 0.2901 (OUTLIER) cc_final: 0.2341 (pm20) REVERT: d 701 MET cc_start: 0.3352 (mmm) cc_final: 0.3119 (mmt) REVERT: e 181 MET cc_start: 0.2539 (mmp) cc_final: 0.1856 (mmt) REVERT: e 959 LYS cc_start: 0.3412 (mmtp) cc_final: 0.3164 (tttt) REVERT: f 301 ARG cc_start: -0.0747 (OUTLIER) cc_final: -0.4472 (mmm160) REVERT: f 627 MET cc_start: 0.2668 (ppp) cc_final: 0.1383 (pmm) REVERT: g 65 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7585 (t80) REVERT: g 370 ILE cc_start: 0.4638 (OUTLIER) cc_final: 0.4429 (mm) REVERT: g 681 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6429 (mp) REVERT: g 685 TYR cc_start: 0.5309 (m-80) cc_final: 0.4745 (m-80) REVERT: g 837 HIS cc_start: 0.3146 (OUTLIER) cc_final: 0.2394 (p90) REVERT: h 130 MET cc_start: 0.0990 (pmm) cc_final: -0.0422 (ptt) REVERT: h 344 ILE cc_start: 0.6416 (mt) cc_final: 0.6128 (mt) REVERT: h 481 MET cc_start: 0.1968 (ppp) cc_final: 0.0895 (tmm) REVERT: h 535 MET cc_start: 0.2524 (OUTLIER) cc_final: 0.0876 (pmm) REVERT: h 574 MET cc_start: 0.5475 (tpt) cc_final: 0.5083 (tpp) REVERT: h 609 GLN cc_start: 0.7298 (tm-30) cc_final: 0.7018 (tm-30) REVERT: h 667 MET cc_start: -0.2438 (ttm) cc_final: -0.2851 (ttm) REVERT: h 838 ILE cc_start: 0.7879 (mt) cc_final: 0.7610 (mp) REVERT: h 853 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4296 (tt) REVERT: h 897 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7426 (t) REVERT: i 25 MET cc_start: 0.2306 (tpp) cc_final: 0.1393 (tmm) REVERT: i 137 MET cc_start: -0.0384 (mtt) cc_final: -0.1075 (mmt) REVERT: i 441 MET cc_start: 0.1016 (tpt) cc_final: 0.0129 (tpt) REVERT: i 486 MET cc_start: 0.8044 (tpt) cc_final: 0.7826 (ttt) REVERT: i 519 MET cc_start: 0.3066 (mmt) cc_final: 0.2654 (mpp) REVERT: i 601 HIS cc_start: -0.0987 (OUTLIER) cc_final: -0.2007 (t70) REVERT: k 299 MET cc_start: 0.4370 (pmm) cc_final: 0.3959 (ppp) REVERT: k 372 MET cc_start: -0.2505 (tmm) cc_final: -0.5180 (ptt) REVERT: m 689 LEU cc_start: -0.2087 (mt) cc_final: -0.2411 (mp) outliers start: 194 outliers final: 93 residues processed: 784 average time/residue: 0.6712 time to fit residues: 933.3156 Evaluate side-chains 692 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 583 time to evaluate : 6.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 79 LEU Chi-restraints excluded: chain p residue 214 SER Chi-restraints excluded: chain p residue 284 VAL Chi-restraints excluded: chain p residue 397 ILE Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 145 TYR Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1162 MET Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2092 MET Chi-restraints excluded: chain a residue 2146 GLU Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain a residue 2184 LEU Chi-restraints excluded: chain b residue 457 SER Chi-restraints excluded: chain b residue 476 PHE Chi-restraints excluded: chain b residue 479 MET Chi-restraints excluded: chain b residue 592 LEU Chi-restraints excluded: chain b residue 646 THR Chi-restraints excluded: chain b residue 737 ASP Chi-restraints excluded: chain b residue 853 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain d residue 386 GLU Chi-restraints excluded: chain d residue 498 THR Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 694 SER Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 901 THR Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 442 LEU Chi-restraints excluded: chain e residue 452 HIS Chi-restraints excluded: chain e residue 574 PHE Chi-restraints excluded: chain e residue 610 LEU Chi-restraints excluded: chain e residue 613 LEU Chi-restraints excluded: chain e residue 640 SER Chi-restraints excluded: chain e residue 659 LEU Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 812 VAL Chi-restraints excluded: chain e residue 816 LEU Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 54 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 267 LEU Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 301 ARG Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain g residue 31 LYS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 151 ASP Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 234 SER Chi-restraints excluded: chain g residue 370 ILE Chi-restraints excluded: chain g residue 543 LYS Chi-restraints excluded: chain g residue 544 GLU Chi-restraints excluded: chain g residue 635 ILE Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 681 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 910 VAL Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 276 GLU Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain h residue 401 VAL Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 508 ASN Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 608 ARG Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 788 VAL Chi-restraints excluded: chain h residue 848 GLN Chi-restraints excluded: chain h residue 853 LEU Chi-restraints excluded: chain h residue 888 CYS Chi-restraints excluded: chain h residue 889 SER Chi-restraints excluded: chain h residue 897 VAL Chi-restraints excluded: chain h residue 921 SER Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 990 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 195 GLN Chi-restraints excluded: chain i residue 468 HIS Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain i residue 643 LEU Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 437 MET Chi-restraints excluded: chain k residue 493 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 889 optimal weight: 40.0000 chunk 606 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 795 optimal weight: 0.9990 chunk 440 optimal weight: 0.9980 chunk 911 optimal weight: 10.0000 chunk 738 optimal weight: 9.9990 chunk 1 optimal weight: 0.0570 chunk 545 optimal weight: 8.9990 chunk 958 optimal weight: 20.0000 chunk 269 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1889 HIS ** a1893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 723 HIS d 756 GLN d 859 ASN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 HIS e 451 HIS e 662 HIS ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 586 GLN g 203 HIS ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN ** g 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 178 GLN h 695 GLN ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4271 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 79542 Z= 0.185 Angle : 0.605 13.065 108531 Z= 0.297 Chirality : 0.041 0.365 13163 Planarity : 0.004 0.070 14182 Dihedral : 4.143 57.152 11625 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 2.60 % Allowed : 20.86 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 0.69 (0.08), residues: 10951 helix: 1.40 (0.07), residues: 6536 sheet: -0.67 (0.23), residues: 485 loop : -0.99 (0.10), residues: 3930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP d 679 HIS 0.028 0.001 HIS e 452 PHE 0.027 0.002 PHE p 538 TYR 0.040 0.002 TYR h 260 ARG 0.011 0.000 ARG a 977 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 600 time to evaluate : 6.828 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: 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: p 397 ILE cc_start: 0.5367 (OUTLIER) cc_final: 0.5054 (tt) REVERT: q 239 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6335 (ttm-80) REVERT: a 1131 MET cc_start: -0.4175 (tpp) cc_final: -0.4512 (ptm) REVERT: a 1223 MET cc_start: 0.3402 (tpp) cc_final: 0.3131 (mmt) REVERT: a 1286 MET cc_start: -0.6086 (tpt) cc_final: -0.6996 (tpt) REVERT: a 1970 ASN cc_start: 0.2364 (OUTLIER) cc_final: 0.1655 (t0) REVERT: b 348 MET cc_start: 0.7945 (mmm) cc_final: 0.7640 (mmm) REVERT: b 479 MET cc_start: -0.0004 (OUTLIER) cc_final: -0.0396 (tmm) REVERT: b 1084 MET cc_start: 0.8209 (mtt) cc_final: 0.7968 (mtt) REVERT: b 1195 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8068 (mm-30) REVERT: d 400 MET cc_start: 0.4026 (OUTLIER) cc_final: 0.3649 (ptt) REVERT: d 750 MET cc_start: 0.0310 (tpt) cc_final: -0.0625 (ptp) REVERT: e 415 MET cc_start: 0.2619 (OUTLIER) cc_final: 0.2328 (mmm) REVERT: f 179 MET cc_start: 0.4267 (OUTLIER) cc_final: 0.4061 (ptt) REVERT: f 627 MET cc_start: 0.2652 (ppp) cc_final: 0.1649 (pmm) REVERT: g 47 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7858 (mpp80) REVERT: g 65 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7714 (t80) REVERT: g 837 HIS cc_start: 0.3511 (OUTLIER) cc_final: 0.2906 (p90) REVERT: h 130 MET cc_start: 0.0805 (pmm) cc_final: -0.0534 (ptt) REVERT: h 535 MET cc_start: 0.2344 (OUTLIER) cc_final: 0.0709 (pmm) REVERT: h 574 MET cc_start: 0.5597 (tpt) cc_final: 0.5151 (tpp) REVERT: h 609 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6891 (tm-30) REVERT: h 667 MET cc_start: -0.2123 (OUTLIER) cc_final: -0.2556 (ttm) REVERT: h 838 ILE cc_start: 0.7935 (mt) cc_final: 0.7657 (mp) REVERT: h 853 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4152 (tt) REVERT: i 25 MET cc_start: 0.2755 (tpp) cc_final: 0.1343 (tmm) REVERT: i 108 MET cc_start: 0.0937 (OUTLIER) cc_final: -0.0587 (mmp) REVERT: i 441 MET cc_start: 0.1150 (tpt) cc_final: 0.0820 (tpp) REVERT: i 519 MET cc_start: 0.2924 (mmt) cc_final: 0.2250 (mpp) REVERT: i 601 HIS cc_start: -0.1510 (OUTLIER) cc_final: -0.1935 (t-170) REVERT: i 642 MET cc_start: 0.8482 (mmp) cc_final: 0.8043 (pmm) REVERT: k 30 MET cc_start: 0.5814 (ppp) cc_final: 0.5367 (ppp) REVERT: k 181 MET cc_start: 0.1751 (mtp) cc_final: 0.1197 (ptp) REVERT: k 299 MET cc_start: 0.4538 (pmm) cc_final: 0.4068 (ppp) REVERT: k 372 MET cc_start: -0.2453 (tmm) cc_final: -0.5126 (ptt) REVERT: m 682 ARG cc_start: 0.1624 (mmm160) cc_final: 0.0897 (mmm160) REVERT: m 689 LEU cc_start: -0.1695 (mt) cc_final: -0.2011 (mp) outliers start: 183 outliers final: 106 residues processed: 732 average time/residue: 0.6805 time to fit residues: 883.6162 Evaluate side-chains 688 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 567 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 214 SER Chi-restraints excluded: chain p residue 287 PHE Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 397 ILE Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 145 TYR Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 239 ARG Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1257 SER Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 476 PHE Chi-restraints excluded: chain b residue 479 MET Chi-restraints excluded: chain b residue 592 LEU Chi-restraints excluded: chain b residue 646 THR Chi-restraints excluded: chain b residue 650 LEU Chi-restraints excluded: chain b residue 853 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain d residue 400 MET Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 498 THR Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 636 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 838 THR Chi-restraints excluded: chain d residue 901 THR Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 442 LEU Chi-restraints excluded: chain e residue 610 LEU Chi-restraints excluded: chain e residue 613 LEU Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 812 VAL Chi-restraints excluded: chain e residue 816 LEU Chi-restraints excluded: chain e residue 847 ILE Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 145 HIS Chi-restraints excluded: chain f residue 179 MET Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain g residue 31 LYS Chi-restraints excluded: chain g residue 47 ARG Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 370 ILE Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 605 THR Chi-restraints excluded: chain g residue 635 ILE Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 699 THR Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 910 VAL Chi-restraints excluded: chain h residue 176 GLN Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain h residue 424 ARG Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 508 ASN Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 608 ARG Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 723 GLN Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 788 VAL Chi-restraints excluded: chain h residue 848 GLN Chi-restraints excluded: chain h residue 853 LEU Chi-restraints excluded: chain h residue 888 CYS Chi-restraints excluded: chain h residue 889 SER Chi-restraints excluded: chain h residue 921 SER Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 941 LEU Chi-restraints excluded: chain h residue 990 MET Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 195 GLN Chi-restraints excluded: chain i residue 429 TYR Chi-restraints excluded: chain i residue 468 HIS Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain i residue 651 VAL Chi-restraints excluded: chain k residue 52 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 437 MET Chi-restraints excluded: chain k residue 465 MET Chi-restraints excluded: chain k residue 493 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 359 optimal weight: 0.9990 chunk 961 optimal weight: 40.0000 chunk 211 optimal weight: 4.9990 chunk 627 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 1069 optimal weight: 6.9990 chunk 887 optimal weight: 10.0000 chunk 495 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 353 optimal weight: 0.8980 chunk 561 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1893 HIS ** a2087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 859 ASN d 864 GLN ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 698 HIS ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 ASN g 202 GLN ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 355 ASN g 369 ASN g 516 GLN g 532 GLN g 570 HIS ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 673 GLN ** g 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 454 GLN h 946 HIS ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 139 HIS k 203 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4425 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 79542 Z= 0.223 Angle : 0.627 12.014 108531 Z= 0.311 Chirality : 0.042 0.252 13163 Planarity : 0.004 0.070 14182 Dihedral : 4.134 61.696 11625 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.94 % Rotamer: Outliers : 3.21 % Allowed : 20.55 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 0.70 (0.08), residues: 10951 helix: 1.42 (0.07), residues: 6555 sheet: -0.69 (0.23), residues: 507 loop : -0.99 (0.10), residues: 3889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 679 HIS 0.016 0.001 HIS a1893 PHE 0.052 0.002 PHE e 931 TYR 0.043 0.002 TYR g 752 ARG 0.011 0.001 ARG a 977 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 600 time to evaluate : 8.477 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: 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: p 208 MET cc_start: 0.0830 (ptt) cc_final: 0.0306 (ttp) REVERT: p 397 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5272 (tt) REVERT: q 65 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.4793 (tp) REVERT: q 245 MET cc_start: 0.3167 (OUTLIER) cc_final: 0.2913 (mpp) REVERT: q 276 MET cc_start: 0.7729 (tmm) cc_final: 0.7499 (ttp) REVERT: a 1131 MET cc_start: -0.3971 (tpp) cc_final: -0.4493 (ptt) REVERT: a 1223 MET cc_start: 0.3544 (tpp) cc_final: 0.3329 (mmt) REVERT: a 1286 MET cc_start: -0.6019 (tpt) cc_final: -0.6810 (tpt) REVERT: a 1970 ASN cc_start: 0.2339 (OUTLIER) cc_final: 0.1749 (t0) REVERT: b 74 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.1969 (mt) REVERT: b 348 MET cc_start: 0.8008 (mmm) cc_final: 0.7669 (mmm) REVERT: b 479 MET cc_start: 0.0362 (OUTLIER) cc_final: -0.0162 (tmm) REVERT: b 517 MET cc_start: 0.7154 (ptm) cc_final: 0.6756 (mmt) REVERT: b 1195 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7992 (mm-30) REVERT: d 400 MET cc_start: 0.4163 (ptt) cc_final: 0.3898 (ptt) REVERT: d 750 MET cc_start: 0.1444 (tpt) cc_final: 0.0657 (ptp) REVERT: e 181 MET cc_start: 0.1310 (mmt) cc_final: 0.0205 (mmt) REVERT: e 406 LEU cc_start: 0.9211 (mt) cc_final: 0.9001 (pp) REVERT: e 415 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2698 (mmm) REVERT: e 510 THR cc_start: 0.1874 (OUTLIER) cc_final: 0.1432 (t) REVERT: e 927 MET cc_start: 0.0976 (tpp) cc_final: 0.0288 (ptt) REVERT: f 179 MET cc_start: 0.4015 (OUTLIER) cc_final: 0.3760 (ptt) REVERT: f 301 ARG cc_start: -0.0263 (OUTLIER) cc_final: -0.4719 (mmp-170) REVERT: f 627 MET cc_start: 0.2813 (ppp) cc_final: 0.1915 (pmm) REVERT: g 47 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8026 (mpp80) REVERT: g 65 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.7957 (t80) REVERT: g 94 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8634 (pp) REVERT: g 257 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5016 (mt) REVERT: g 675 MET cc_start: 0.7499 (ttt) cc_final: 0.7244 (ttm) REVERT: h 130 MET cc_start: 0.0660 (pmm) cc_final: -0.0861 (ptt) REVERT: h 177 MET cc_start: 0.2488 (tmm) cc_final: 0.2206 (ppp) REVERT: h 213 TYR cc_start: 0.6873 (m-80) cc_final: 0.6619 (m-80) REVERT: h 343 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7631 (mm-40) REVERT: h 535 MET cc_start: 0.2306 (OUTLIER) cc_final: 0.0693 (pmm) REVERT: h 609 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6822 (tm-30) REVERT: h 667 MET cc_start: -0.2223 (OUTLIER) cc_final: -0.2655 (ttm) REVERT: h 842 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6827 (mt) REVERT: h 876 TYR cc_start: 0.4222 (OUTLIER) cc_final: 0.3744 (t80) REVERT: h 925 MET cc_start: 0.9104 (mtm) cc_final: 0.8663 (mtt) REVERT: i 25 MET cc_start: 0.2776 (tpp) cc_final: 0.1498 (tmm) REVERT: i 108 MET cc_start: 0.0524 (OUTLIER) cc_final: -0.0506 (mmp) REVERT: i 441 MET cc_start: 0.1789 (tpt) cc_final: 0.1082 (tpt) REVERT: i 519 MET cc_start: 0.2831 (mmt) cc_final: 0.2183 (mpp) REVERT: i 601 HIS cc_start: -0.1417 (OUTLIER) cc_final: -0.1872 (t-170) REVERT: i 642 MET cc_start: 0.8372 (mmp) cc_final: 0.7867 (pmm) REVERT: k 30 MET cc_start: 0.5872 (ppp) cc_final: 0.5467 (ppp) REVERT: k 181 MET cc_start: 0.1843 (mtp) cc_final: 0.1303 (ptp) REVERT: k 299 MET cc_start: 0.4712 (pmm) cc_final: 0.4193 (ppp) REVERT: k 372 MET cc_start: -0.2320 (tmm) cc_final: -0.4870 (ptt) REVERT: m 689 LEU cc_start: -0.1694 (mt) cc_final: -0.2034 (mp) outliers start: 226 outliers final: 121 residues processed: 778 average time/residue: 0.6970 time to fit residues: 961.2815 Evaluate side-chains 701 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 560 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 11 TYR Chi-restraints excluded: chain p residue 79 LEU Chi-restraints excluded: chain p residue 172 ASN Chi-restraints excluded: chain p residue 214 SER Chi-restraints excluded: chain p residue 287 PHE Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 397 ILE Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 93 SER Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 145 TYR Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 234 LEU Chi-restraints excluded: chain q residue 245 MET Chi-restraints excluded: chain q residue 256 VAL Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain r residue 1058 MET Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1257 SER Chi-restraints excluded: chain a residue 1494 LEU Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2050 TYR Chi-restraints excluded: chain a residue 2094 SER Chi-restraints excluded: chain a residue 2146 GLU Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 435 MET Chi-restraints excluded: chain b residue 476 PHE Chi-restraints excluded: chain b residue 479 MET Chi-restraints excluded: chain b residue 592 LEU Chi-restraints excluded: chain b residue 646 THR Chi-restraints excluded: chain b residue 650 LEU Chi-restraints excluded: chain b residue 800 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 498 THR Chi-restraints excluded: chain d residue 525 LEU Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 694 SER Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 838 THR Chi-restraints excluded: chain d residue 901 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 442 LEU Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 510 THR Chi-restraints excluded: chain e residue 613 LEU Chi-restraints excluded: chain e residue 627 SER Chi-restraints excluded: chain e residue 647 LEU Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 812 VAL Chi-restraints excluded: chain e residue 816 LEU Chi-restraints excluded: chain e residue 847 ILE Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 54 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 145 HIS Chi-restraints excluded: chain f residue 179 MET Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 301 ARG Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain g residue 31 LYS Chi-restraints excluded: chain g residue 47 ARG Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 234 SER Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 370 ILE Chi-restraints excluded: chain g residue 543 LYS Chi-restraints excluded: chain g residue 570 HIS Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 662 GLN Chi-restraints excluded: chain g residue 699 THR Chi-restraints excluded: chain g residue 767 THR Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 910 VAL Chi-restraints excluded: chain h residue 176 GLN Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 424 ARG Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 520 VAL Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 788 VAL Chi-restraints excluded: chain h residue 822 VAL Chi-restraints excluded: chain h residue 842 ILE Chi-restraints excluded: chain h residue 876 TYR Chi-restraints excluded: chain h residue 887 CYS Chi-restraints excluded: chain h residue 888 CYS Chi-restraints excluded: chain h residue 889 SER Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 941 LEU Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 429 TYR Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain k residue 52 THR Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 493 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 1030 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 609 optimal weight: 0.6980 chunk 780 optimal weight: 6.9990 chunk 604 optimal weight: 0.9990 chunk 899 optimal weight: 9.9990 chunk 597 optimal weight: 4.9990 chunk 1065 optimal weight: 8.9990 chunk 666 optimal weight: 0.9980 chunk 649 optimal weight: 4.9990 chunk 491 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 539 ASN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1381 GLN a1893 HIS a2089 GLN ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 700 GLN ** b 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 475 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 626 HIS ** d 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 859 ASN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 900 HIS d 918 ASN ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 963 GLN g 89 GLN g 93 HIS g 202 GLN g 355 ASN ** g 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 673 GLN ** g 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 826 GLN g 875 ASN h 178 GLN ** h 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 922 HIS i 37 ASN i 45 GLN i 116 HIS ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 79542 Z= 0.308 Angle : 0.696 14.836 108531 Z= 0.355 Chirality : 0.044 0.336 13163 Planarity : 0.005 0.117 14182 Dihedral : 4.345 65.929 11625 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.36 % Favored : 95.63 % Rotamer: Outliers : 3.11 % Allowed : 21.25 % Favored : 75.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.98 % 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: 0.51 (0.08), residues: 10951 helix: 1.23 (0.07), residues: 6556 sheet: -0.74 (0.23), residues: 493 loop : -1.01 (0.10), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP r1037 HIS 0.128 0.002 HIS g 570 PHE 0.041 0.002 PHE h 442 TYR 0.046 0.002 TYR g 752 ARG 0.043 0.001 ARG a1777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 576 time to evaluate : 7.257 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 208 MET cc_start: 0.1336 (ptt) cc_final: 0.0468 (ptt) REVERT: p 350 MET cc_start: 0.0132 (mmm) cc_final: -0.0217 (mmm) REVERT: p 397 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5540 (tt) REVERT: q 69 PHE cc_start: 0.5686 (m-80) cc_final: 0.5420 (m-10) REVERT: q 83 MET cc_start: 0.6850 (mmm) cc_final: 0.5905 (mpp) REVERT: q 245 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4772 (mpp) REVERT: a 1131 MET cc_start: -0.3821 (tpp) cc_final: -0.4427 (ptm) REVERT: a 1207 ASP cc_start: -0.0490 (OUTLIER) cc_final: -0.1516 (p0) REVERT: a 1970 ASN cc_start: 0.2812 (OUTLIER) cc_final: 0.2394 (t0) REVERT: b 348 MET cc_start: 0.7922 (mmm) cc_final: 0.7550 (mmm) REVERT: b 770 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8266 (tp-100) REVERT: b 772 MET cc_start: 0.8566 (mmm) cc_final: 0.8366 (mmm) REVERT: d 400 MET cc_start: 0.4641 (ptt) cc_final: 0.4375 (ptt) REVERT: d 561 MET cc_start: 0.8593 (tpp) cc_final: 0.8126 (mpp) REVERT: d 694 SER cc_start: 0.3145 (OUTLIER) cc_final: 0.2925 (p) REVERT: d 750 MET cc_start: 0.2053 (tpt) cc_final: 0.1696 (ptp) REVERT: e 181 MET cc_start: 0.1566 (mmt) cc_final: 0.0379 (mmt) REVERT: e 415 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.3096 (mmm) REVERT: e 510 THR cc_start: 0.3053 (OUTLIER) cc_final: 0.2789 (t) REVERT: e 817 VAL cc_start: 0.8081 (t) cc_final: 0.7768 (p) REVERT: e 844 ASP cc_start: 0.6290 (m-30) cc_final: 0.5964 (t0) REVERT: e 927 MET cc_start: 0.1099 (tpp) cc_final: 0.0276 (ptt) REVERT: f 24 TYR cc_start: 0.3133 (OUTLIER) cc_final: 0.2401 (m-80) REVERT: f 33 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.5446 (mm-30) REVERT: f 179 MET cc_start: 0.4893 (OUTLIER) cc_final: 0.4688 (ptt) REVERT: f 433 MET cc_start: 0.2357 (ptp) cc_final: 0.2116 (ptp) REVERT: f 627 MET cc_start: 0.2513 (ppp) cc_final: 0.1519 (pmm) REVERT: g 65 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8149 (t80) REVERT: g 91 GLU cc_start: 0.7737 (tp30) cc_final: 0.7513 (tp30) REVERT: g 673 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8713 (pp30) REVERT: g 675 MET cc_start: 0.7638 (ttt) cc_final: 0.7386 (ttm) REVERT: g 837 HIS cc_start: 0.5111 (OUTLIER) cc_final: 0.4259 (p90) REVERT: h 130 MET cc_start: 0.0736 (pmm) cc_final: -0.0684 (ptt) REVERT: h 343 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7732 (mm-40) REVERT: h 435 LEU cc_start: 0.7073 (mt) cc_final: 0.6373 (tt) REVERT: h 535 MET cc_start: 0.2511 (OUTLIER) cc_final: 0.0951 (pmm) REVERT: h 574 MET cc_start: 0.5570 (tpt) cc_final: 0.5170 (tpp) REVERT: h 609 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7155 (tm-30) REVERT: h 611 MET cc_start: 0.4770 (mmp) cc_final: 0.4327 (mmp) REVERT: h 667 MET cc_start: -0.1772 (OUTLIER) cc_final: -0.2281 (ttm) REVERT: h 842 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7986 (mt) REVERT: h 925 MET cc_start: 0.9115 (mtm) cc_final: 0.8744 (mtt) REVERT: i 25 MET cc_start: 0.3054 (tpp) cc_final: 0.1813 (tmm) REVERT: i 108 MET cc_start: 0.0490 (OUTLIER) cc_final: -0.0636 (mmp) REVERT: i 441 MET cc_start: 0.2368 (tpt) cc_final: 0.1596 (tpt) REVERT: i 519 MET cc_start: 0.2823 (mmt) cc_final: 0.2157 (mpp) REVERT: i 601 HIS cc_start: -0.1534 (OUTLIER) cc_final: -0.1950 (t-170) REVERT: i 642 MET cc_start: 0.8511 (mmp) cc_final: 0.8000 (pmm) REVERT: k 30 MET cc_start: 0.5621 (ppp) cc_final: 0.5292 (ppp) REVERT: k 181 MET cc_start: 0.1807 (mtp) cc_final: 0.1564 (ptp) REVERT: k 299 MET cc_start: 0.4701 (pmm) cc_final: 0.4077 (ppp) REVERT: k 372 MET cc_start: -0.2177 (OUTLIER) cc_final: -0.4891 (ptt) REVERT: k 518 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.8750 (t70) REVERT: m 682 ARG cc_start: 0.1790 (mmm-85) cc_final: 0.1325 (mmm160) outliers start: 219 outliers final: 117 residues processed: 744 average time/residue: 0.7033 time to fit residues: 931.2877 Evaluate side-chains 670 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 532 time to evaluate : 6.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 79 LEU Chi-restraints excluded: chain p residue 214 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 397 ILE Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain p residue 585 VAL Chi-restraints excluded: chain q residue 27 GLN Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 93 SER Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 219 THR Chi-restraints excluded: chain q residue 245 MET Chi-restraints excluded: chain q residue 256 VAL Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1207 ASP Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1257 SER Chi-restraints excluded: chain a residue 1281 MET Chi-restraints excluded: chain a residue 1494 LEU Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2094 SER Chi-restraints excluded: chain a residue 2111 MET Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain b residue 299 VAL Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 770 GLN Chi-restraints excluded: chain b residue 800 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain b residue 1199 MET Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 498 THR Chi-restraints excluded: chain d residue 525 LEU Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 685 LEU Chi-restraints excluded: chain d residue 694 SER Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 838 THR Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 442 LEU Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 510 THR Chi-restraints excluded: chain e residue 613 LEU Chi-restraints excluded: chain e residue 647 LEU Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 812 VAL Chi-restraints excluded: chain e residue 847 ILE Chi-restraints excluded: chain e residue 877 LEU Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain e residue 997 ASP Chi-restraints excluded: chain f residue 24 TYR Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 179 MET Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 267 LEU Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 151 ASP Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 414 ASN Chi-restraints excluded: chain g residue 452 CYS Chi-restraints excluded: chain g residue 556 GLU Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 605 THR Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 673 GLN Chi-restraints excluded: chain g residue 699 THR Chi-restraints excluded: chain g residue 752 TYR Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 835 VAL Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 924 THR Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 424 ARG Chi-restraints excluded: chain h residue 453 LEU Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 508 ASN Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 766 GLU Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 822 VAL Chi-restraints excluded: chain h residue 842 ILE Chi-restraints excluded: chain h residue 897 VAL Chi-restraints excluded: chain h residue 935 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain k residue 52 THR Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 372 MET Chi-restraints excluded: chain k residue 518 HIS Chi-restraints excluded: chain m residue 661 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 658 optimal weight: 0.0770 chunk 425 optimal weight: 0.7980 chunk 636 optimal weight: 3.9990 chunk 320 optimal weight: 0.0000 chunk 209 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 677 optimal weight: 0.8980 chunk 725 optimal weight: 0.9980 chunk 526 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 837 optimal weight: 9.9990 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1381 GLN a1426 HIS a1893 HIS ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 GLN ** b 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 665 ASN b 707 HIS b 747 ASN b 756 GLN ** b1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 680 ASN ** d 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 884 ASN d 918 ASN ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 963 GLN g 89 GLN g 178 ASN ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN g 516 GLN ** g 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 708 GLN ** g 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 848 GLN h 178 GLN h 251 GLN h 388 ASN ** h 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 195 GLN ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4613 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 79542 Z= 0.190 Angle : 0.640 22.516 108531 Z= 0.314 Chirality : 0.042 0.466 13163 Planarity : 0.004 0.060 14182 Dihedral : 4.124 65.218 11625 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.06 % Allowed : 22.61 % Favored : 75.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.98 % 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: 0.72 (0.08), residues: 10951 helix: 1.40 (0.07), residues: 6555 sheet: -0.50 (0.24), residues: 477 loop : -0.95 (0.10), residues: 3919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP r1037 HIS 0.017 0.001 HIS a1893 PHE 0.039 0.002 PHE e 931 TYR 0.047 0.002 TYR g 752 ARG 0.011 0.000 ARG a1777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 565 time to evaluate : 6.837 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: symmetry clash revert: symmetry clash REVERT: p 291 MET cc_start: 0.3921 (ptp) cc_final: 0.3683 (ptp) REVERT: p 350 MET cc_start: 0.0077 (mmm) cc_final: -0.0294 (mmm) REVERT: p 397 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.5417 (tt) REVERT: q 65 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5215 (tp) REVERT: q 69 PHE cc_start: 0.5179 (m-80) cc_final: 0.4807 (m-80) REVERT: q 80 TYR cc_start: 0.4031 (m-10) cc_final: 0.3656 (m-80) REVERT: q 245 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4369 (mpp) REVERT: a 1131 MET cc_start: -0.3771 (tpp) cc_final: -0.4424 (ptm) REVERT: a 1162 MET cc_start: -0.1062 (tmm) cc_final: -0.1429 (tmm) REVERT: a 1286 MET cc_start: -0.5682 (tpp) cc_final: -0.6592 (tpt) REVERT: a 1970 ASN cc_start: 0.2741 (OUTLIER) cc_final: 0.2332 (t0) REVERT: b 348 MET cc_start: 0.7904 (mmm) cc_final: 0.7525 (mmm) REVERT: b 576 TRP cc_start: 0.2372 (OUTLIER) cc_final: 0.1817 (m100) REVERT: d 400 MET cc_start: 0.4521 (ptt) cc_final: 0.4250 (ptt) REVERT: d 561 MET cc_start: 0.8457 (tpp) cc_final: 0.7983 (mpp) REVERT: d 750 MET cc_start: 0.1867 (tpt) cc_final: 0.1630 (ptp) REVERT: e 181 MET cc_start: 0.1392 (mmt) cc_final: 0.0232 (mmt) REVERT: e 415 MET cc_start: 0.3547 (OUTLIER) cc_final: 0.3183 (mmm) REVERT: e 510 THR cc_start: 0.2615 (OUTLIER) cc_final: 0.2325 (t) REVERT: e 519 LEU cc_start: 0.8194 (mt) cc_final: 0.7992 (mt) REVERT: e 817 VAL cc_start: 0.8288 (t) cc_final: 0.8028 (p) REVERT: e 844 ASP cc_start: 0.6101 (m-30) cc_final: 0.5730 (t0) REVERT: f 179 MET cc_start: 0.4814 (OUTLIER) cc_final: 0.4603 (ptt) REVERT: f 301 ARG cc_start: -0.0318 (OUTLIER) cc_final: -0.4415 (mmm160) REVERT: f 349 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: f 627 MET cc_start: 0.2560 (OUTLIER) cc_final: 0.1593 (pmm) REVERT: g 27 MET cc_start: 0.8649 (mmm) cc_final: 0.8173 (mmp) REVERT: g 65 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8085 (t80) REVERT: g 94 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8704 (pp) REVERT: g 257 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6139 (mt) REVERT: g 675 MET cc_start: 0.7755 (ttt) cc_final: 0.7516 (ttm) REVERT: g 804 ILE cc_start: 0.5423 (mp) cc_final: 0.5164 (tt) REVERT: h 130 MET cc_start: 0.0701 (pmm) cc_final: -0.0742 (ptt) REVERT: h 535 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.0895 (pmm) REVERT: h 574 MET cc_start: 0.5271 (tpt) cc_final: 0.4960 (tpp) REVERT: h 609 GLN cc_start: 0.7316 (tm-30) cc_final: 0.7037 (tm-30) REVERT: h 667 MET cc_start: -0.1759 (OUTLIER) cc_final: -0.2240 (ttm) REVERT: h 842 ILE cc_start: 0.8200 (mt) cc_final: 0.7977 (mt) REVERT: h 876 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.4680 (t80) REVERT: h 925 MET cc_start: 0.9024 (mtm) cc_final: 0.8669 (mtt) REVERT: i 25 MET cc_start: 0.3211 (tpp) cc_final: 0.1776 (tmm) REVERT: i 108 MET cc_start: 0.0002 (OUTLIER) cc_final: -0.0574 (mmp) REVERT: i 441 MET cc_start: 0.2120 (tpt) cc_final: 0.1372 (tpt) REVERT: i 519 MET cc_start: 0.3143 (mmt) cc_final: 0.2527 (mpp) REVERT: i 601 HIS cc_start: -0.1576 (OUTLIER) cc_final: -0.1985 (t-170) REVERT: i 642 MET cc_start: 0.8506 (mmp) cc_final: 0.7992 (pmm) REVERT: k 30 MET cc_start: 0.5817 (ppp) cc_final: 0.5397 (ppp) REVERT: k 299 MET cc_start: 0.4879 (pmm) cc_final: 0.4350 (ppp) REVERT: k 372 MET cc_start: -0.2343 (tmm) cc_final: -0.4996 (ptt) REVERT: k 518 HIS cc_start: 0.9388 (OUTLIER) cc_final: 0.8751 (t70) REVERT: m 682 ARG cc_start: 0.2050 (mmm-85) cc_final: 0.1590 (mmm160) REVERT: m 689 LEU cc_start: -0.1734 (mt) cc_final: -0.2154 (mp) outliers start: 145 outliers final: 87 residues processed: 675 average time/residue: 0.7047 time to fit residues: 848.3013 Evaluate side-chains 642 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 535 time to evaluate : 6.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 171 ARG Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 397 ILE Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain q residue 27 GLN Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 131 ASP Chi-restraints excluded: chain q residue 180 ILE Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 245 MET Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain a residue 984 VAL Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1281 MET Chi-restraints excluded: chain a residue 1494 LEU Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2111 MET Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain b residue 383 VAL Chi-restraints excluded: chain b residue 576 TRP Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 729 CYS Chi-restraints excluded: chain b residue 853 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain b residue 1199 MET Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 525 LEU Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 838 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 485 CYS Chi-restraints excluded: chain e residue 510 THR Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 812 VAL Chi-restraints excluded: chain e residue 847 ILE Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 179 MET Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 292 ASP Chi-restraints excluded: chain f residue 301 ARG Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 349 GLN Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain f residue 627 MET Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 370 ILE Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 688 LEU Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 853 ASN Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 914 ASN Chi-restraints excluded: chain g residue 935 TYR Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 424 ARG Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 612 LEU Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 753 TYR Chi-restraints excluded: chain h residue 876 TYR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 429 TYR Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain i residue 651 VAL Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 437 MET Chi-restraints excluded: chain k residue 518 HIS Chi-restraints excluded: chain m residue 661 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 968 optimal weight: 10.0000 chunk 1020 optimal weight: 20.0000 chunk 930 optimal weight: 40.0000 chunk 992 optimal weight: 8.9990 chunk 597 optimal weight: 2.9990 chunk 432 optimal weight: 3.9990 chunk 779 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 896 optimal weight: 6.9990 chunk 938 optimal weight: 50.0000 chunk 989 optimal weight: 50.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1061 GLN ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1305 HIS ** a1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1381 GLN ** a1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1893 HIS ** a1981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2058 GLN a2176 GLN ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 534 HIS d 54 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 568 HIS ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 805 GLN d 895 GLN d 918 ASN ** e 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 GLN ** f 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN g 399 GLN ** g 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 437 GLN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 673 GLN ** g 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 330 HIS ** h 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 103 ASN ** i 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 1.0144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.157 79542 Z= 0.656 Angle : 1.109 25.605 108531 Z= 0.569 Chirality : 0.059 0.680 13163 Planarity : 0.008 0.222 14182 Dihedral : 5.551 73.072 11625 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 37.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.01 % Rotamer: Outliers : 2.91 % Allowed : 22.08 % Favored : 75.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.69 (0.08), residues: 10951 helix: 0.21 (0.06), residues: 6500 sheet: -1.36 (0.23), residues: 470 loop : -1.33 (0.10), residues: 3981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP h 548 HIS 0.040 0.003 HIS f 400 PHE 0.105 0.005 PHE e 931 TYR 0.125 0.005 TYR a2050 ARG 0.032 0.002 ARG g 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 541 time to evaluate : 6.724 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 208 MET cc_start: 0.2229 (ptt) cc_final: 0.1948 (ttp) REVERT: p 291 MET cc_start: 0.4846 (ptp) cc_final: 0.4193 (ptp) REVERT: q 245 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6923 (mpp) REVERT: r 1040 ASN cc_start: 0.5698 (OUTLIER) cc_final: 0.5337 (p0) REVERT: a 1207 ASP cc_start: -0.0326 (OUTLIER) cc_final: -0.1482 (p0) REVERT: a 1516 VAL cc_start: 0.7524 (t) cc_final: 0.6242 (t) REVERT: b 256 MET cc_start: -0.2482 (mmt) cc_final: -0.2821 (mmt) REVERT: b 743 MET cc_start: 0.9109 (tpp) cc_final: 0.8641 (mpp) REVERT: b 770 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8624 (tp-100) REVERT: d 400 MET cc_start: 0.5199 (ptt) cc_final: 0.4797 (ptt) REVERT: d 561 MET cc_start: 0.8995 (tpp) cc_final: 0.8178 (mpp) REVERT: d 701 MET cc_start: 0.3315 (mmp) cc_final: 0.3014 (mmt) REVERT: d 784 MET cc_start: 0.5174 (mmm) cc_final: 0.4842 (mmm) REVERT: e 474 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7263 (tt) REVERT: f 627 MET cc_start: 0.3107 (ppp) cc_final: 0.2777 (pmm) REVERT: g 27 MET cc_start: 0.9045 (mmm) cc_final: 0.8479 (mmm) REVERT: g 65 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8076 (t80) REVERT: g 472 MET cc_start: 0.1953 (mmt) cc_final: 0.1489 (mmt) REVERT: g 675 MET cc_start: 0.7055 (ttt) cc_final: 0.6601 (ttt) REVERT: g 748 MET cc_start: 0.3648 (tpt) cc_final: 0.2770 (ptt) REVERT: h 39 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8151 (mmp80) REVERT: h 130 MET cc_start: 0.1337 (pmm) cc_final: -0.0075 (ptt) REVERT: h 174 MET cc_start: 0.7141 (tpp) cc_final: 0.6707 (mmm) REVERT: h 177 MET cc_start: 0.4335 (ppp) cc_final: 0.3917 (ppp) REVERT: h 471 ASP cc_start: 0.8559 (p0) cc_final: 0.8310 (p0) REVERT: h 535 MET cc_start: 0.3260 (OUTLIER) cc_final: 0.1708 (pmm) REVERT: h 574 MET cc_start: 0.6679 (tpt) cc_final: 0.6395 (tpp) REVERT: h 696 LEU cc_start: 0.6845 (mt) cc_final: 0.6544 (mm) REVERT: h 817 THR cc_start: 0.7741 (m) cc_final: 0.7431 (p) REVERT: h 828 ILE cc_start: 0.7123 (mm) cc_final: 0.6902 (mm) REVERT: h 896 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8312 (mp10) REVERT: h 925 MET cc_start: 0.9096 (mtm) cc_final: 0.8788 (mtm) REVERT: i 137 MET cc_start: 0.1649 (mtt) cc_final: 0.1335 (mmt) REVERT: i 409 MET cc_start: 0.2694 (ttt) cc_final: 0.2179 (ppp) REVERT: i 519 MET cc_start: 0.2896 (mmt) cc_final: 0.2330 (mpp) REVERT: i 601 HIS cc_start: -0.0931 (OUTLIER) cc_final: -0.1319 (t-170) REVERT: i 642 MET cc_start: 0.8546 (mmp) cc_final: 0.8045 (pmm) REVERT: k 30 MET cc_start: 0.6108 (ppp) cc_final: 0.5795 (ppp) REVERT: k 372 MET cc_start: -0.2618 (OUTLIER) cc_final: -0.4833 (ptt) REVERT: k 518 HIS cc_start: 0.9410 (OUTLIER) cc_final: 0.8775 (t70) outliers start: 205 outliers final: 125 residues processed: 708 average time/residue: 0.7276 time to fit residues: 914.9415 Evaluate side-chains 618 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 482 time to evaluate : 6.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 171 ARG Chi-restraints excluded: chain p residue 172 ASN Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain p residue 585 VAL Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 118 HIS Chi-restraints excluded: chain q residue 145 TYR Chi-restraints excluded: chain q residue 183 LEU Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 219 THR Chi-restraints excluded: chain q residue 245 MET Chi-restraints excluded: chain q residue 256 VAL Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain r residue 1040 ASN Chi-restraints excluded: chain a residue 984 VAL Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1207 ASP Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1364 MET Chi-restraints excluded: chain a residue 1494 LEU Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 296 SER Chi-restraints excluded: chain b residue 299 VAL Chi-restraints excluded: chain b residue 534 HIS Chi-restraints excluded: chain b residue 571 VAL Chi-restraints excluded: chain b residue 575 ASP Chi-restraints excluded: chain b residue 620 THR Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 729 CYS Chi-restraints excluded: chain b residue 770 GLN Chi-restraints excluded: chain b residue 831 MET Chi-restraints excluded: chain b residue 833 VAL Chi-restraints excluded: chain b residue 853 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 421 ASN Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 525 LEU Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 725 MET Chi-restraints excluded: chain d residue 804 ARG Chi-restraints excluded: chain d residue 805 GLN Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 909 VAL Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 473 PHE Chi-restraints excluded: chain e residue 474 LEU Chi-restraints excluded: chain e residue 488 THR Chi-restraints excluded: chain e residue 508 VAL Chi-restraints excluded: chain e residue 549 LEU Chi-restraints excluded: chain e residue 690 GLN Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 799 TRP Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain e residue 905 GLU Chi-restraints excluded: chain e residue 937 PHE Chi-restraints excluded: chain e residue 1001 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 199 MET Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 349 GLN Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 395 ASP Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 429 LYS Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain f residue 562 ASN Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 151 ASP Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 234 SER Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 414 ASN Chi-restraints excluded: chain g residue 452 CYS Chi-restraints excluded: chain g residue 556 GLU Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 699 THR Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 924 THR Chi-restraints excluded: chain g residue 935 TYR Chi-restraints excluded: chain h residue 213 TYR Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 403 PHE Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 612 LEU Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 822 VAL Chi-restraints excluded: chain h residue 876 TYR Chi-restraints excluded: chain h residue 889 SER Chi-restraints excluded: chain h residue 896 GLN Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 108 MET Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 224 ASN Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 372 MET Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 437 MET Chi-restraints excluded: chain k residue 518 HIS Chi-restraints excluded: chain m residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 651 optimal weight: 1.9990 chunk 1049 optimal weight: 3.9990 chunk 640 optimal weight: 1.9990 chunk 497 optimal weight: 1.9990 chunk 729 optimal weight: 4.9990 chunk 1100 optimal weight: 10.0000 chunk 1013 optimal weight: 40.0000 chunk 876 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 677 optimal weight: 8.9990 chunk 537 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1893 HIS ** a1981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 716 ASN ** d 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN ** g 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 414 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 1.0195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.452 79542 Z= 0.629 Angle : 1.118 59.194 108531 Z= 0.570 Chirality : 0.058 1.126 13163 Planarity : 0.008 0.212 14182 Dihedral : 5.537 73.129 11625 Min Nonbonded Distance : 1.216 Molprobity Statistics. All-atom Clashscore : 39.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 2.28 % Allowed : 23.23 % Favored : 74.48 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.08), residues: 10951 helix: 0.15 (0.06), residues: 6503 sheet: -1.47 (0.23), residues: 472 loop : -1.36 (0.10), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.162 0.004 TRP r1041 HIS 0.312 0.004 HIS b 534 PHE 0.100 0.005 PHE e 931 TYR 0.122 0.005 TYR h 675 ARG 0.069 0.002 ARG g 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21902 Ramachandran restraints generated. 10951 Oldfield, 0 Emsley, 10951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 476 time to evaluate : 6.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: p 208 MET cc_start: 0.2207 (ptt) cc_final: 0.1940 (ttp) REVERT: p 291 MET cc_start: 0.4841 (ptp) cc_final: 0.4188 (ptp) REVERT: q 245 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6838 (mpp) REVERT: a 1483 MET cc_start: 0.8389 (pmm) cc_final: 0.8112 (pmm) REVERT: a 1514 LEU cc_start: 0.3861 (OUTLIER) cc_final: 0.3576 (mm) REVERT: b 256 MET cc_start: -0.2412 (mmt) cc_final: -0.2785 (mmt) REVERT: b 743 MET cc_start: 0.9082 (tpp) cc_final: 0.8632 (mpp) REVERT: b 770 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8613 (tp-100) REVERT: d 386 GLU cc_start: 0.4729 (OUTLIER) cc_final: 0.3810 (pm20) REVERT: d 400 MET cc_start: 0.5128 (ptt) cc_final: 0.4731 (ptt) REVERT: d 561 MET cc_start: 0.8983 (tpp) cc_final: 0.8175 (mpp) REVERT: d 701 MET cc_start: 0.3355 (mmp) cc_final: 0.2995 (mmt) REVERT: e 474 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7219 (tt) REVERT: e 927 MET cc_start: 0.0465 (mtt) cc_final: 0.0033 (ttm) REVERT: f 627 MET cc_start: 0.3110 (OUTLIER) cc_final: 0.2797 (pmm) REVERT: g 27 MET cc_start: 0.8989 (mmm) cc_final: 0.8508 (mmm) REVERT: g 65 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8134 (t80) REVERT: g 472 MET cc_start: 0.1912 (mmt) cc_final: 0.1472 (mmt) REVERT: g 675 MET cc_start: 0.7038 (ttt) cc_final: 0.6618 (ttt) REVERT: g 748 MET cc_start: 0.3797 (tpt) cc_final: 0.2795 (ptt) REVERT: h 39 ARG cc_start: 0.8717 (mmt-90) cc_final: 0.8148 (mmp80) REVERT: h 130 MET cc_start: 0.1335 (pmm) cc_final: -0.0074 (ptt) REVERT: h 174 MET cc_start: 0.7105 (tpp) cc_final: 0.6684 (mmm) REVERT: h 177 MET cc_start: 0.4352 (ppp) cc_final: 0.3963 (ppp) REVERT: h 471 ASP cc_start: 0.8559 (p0) cc_final: 0.8308 (p0) REVERT: h 535 MET cc_start: 0.3219 (OUTLIER) cc_final: 0.1675 (pmm) REVERT: h 574 MET cc_start: 0.6647 (tpt) cc_final: 0.6356 (tpp) REVERT: h 667 MET cc_start: 0.0630 (OUTLIER) cc_final: -0.0030 (ttm) REVERT: h 817 THR cc_start: 0.7746 (m) cc_final: 0.7427 (p) REVERT: h 828 ILE cc_start: 0.7090 (mm) cc_final: 0.6871 (mm) REVERT: h 896 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: h 925 MET cc_start: 0.9100 (mtm) cc_final: 0.8786 (mtm) REVERT: i 108 MET cc_start: 0.0833 (mmm) cc_final: -0.0188 (mmp) REVERT: i 409 MET cc_start: 0.2923 (ttt) cc_final: 0.2408 (ppp) REVERT: i 441 MET cc_start: 0.4511 (mmt) cc_final: 0.2227 (tpp) REVERT: i 519 MET cc_start: 0.2893 (mmt) cc_final: 0.2332 (mpp) REVERT: i 601 HIS cc_start: -0.0932 (OUTLIER) cc_final: -0.1319 (t-170) REVERT: k 30 MET cc_start: 0.6123 (ppp) cc_final: 0.5831 (ppp) REVERT: k 372 MET cc_start: -0.2607 (OUTLIER) cc_final: -0.4851 (ptt) REVERT: k 518 HIS cc_start: 0.9410 (OUTLIER) cc_final: 0.8775 (t70) outliers start: 161 outliers final: 130 residues processed: 604 average time/residue: 0.7364 time to fit residues: 798.2363 Evaluate side-chains 613 residues out of total 9820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 470 time to evaluate : 6.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 60 TYR Chi-restraints excluded: chain p residue 171 ARG Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 463 THR Chi-restraints excluded: chain p residue 483 ILE Chi-restraints excluded: chain p residue 568 THR Chi-restraints excluded: chain p residue 585 VAL Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 118 HIS Chi-restraints excluded: chain q residue 145 TYR Chi-restraints excluded: chain q residue 183 LEU Chi-restraints excluded: chain q residue 218 TYR Chi-restraints excluded: chain q residue 219 THR Chi-restraints excluded: chain q residue 245 MET Chi-restraints excluded: chain q residue 256 VAL Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain r residue 1037 TRP Chi-restraints excluded: chain a residue 984 VAL Chi-restraints excluded: chain a residue 1107 LEU Chi-restraints excluded: chain a residue 1155 SER Chi-restraints excluded: chain a residue 1230 ARG Chi-restraints excluded: chain a residue 1233 ASP Chi-restraints excluded: chain a residue 1364 MET Chi-restraints excluded: chain a residue 1494 LEU Chi-restraints excluded: chain a residue 1495 SER Chi-restraints excluded: chain a residue 1514 LEU Chi-restraints excluded: chain a residue 1660 LEU Chi-restraints excluded: chain a residue 1724 VAL Chi-restraints excluded: chain a residue 1848 ASP Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 1970 ASN Chi-restraints excluded: chain a residue 2153 GLU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 557 ILE Chi-restraints excluded: chain b residue 571 VAL Chi-restraints excluded: chain b residue 575 ASP Chi-restraints excluded: chain b residue 620 THR Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 729 CYS Chi-restraints excluded: chain b residue 770 GLN Chi-restraints excluded: chain b residue 797 MET Chi-restraints excluded: chain b residue 833 VAL Chi-restraints excluded: chain b residue 853 LEU Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 292 SER Chi-restraints excluded: chain d residue 386 GLU Chi-restraints excluded: chain d residue 421 ASN Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 525 LEU Chi-restraints excluded: chain d residue 550 LEU Chi-restraints excluded: chain d residue 668 LEU Chi-restraints excluded: chain d residue 679 TRP Chi-restraints excluded: chain d residue 725 MET Chi-restraints excluded: chain d residue 804 ARG Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 909 VAL Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 210 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain e residue 442 LEU Chi-restraints excluded: chain e residue 473 PHE Chi-restraints excluded: chain e residue 474 LEU Chi-restraints excluded: chain e residue 488 THR Chi-restraints excluded: chain e residue 549 LEU Chi-restraints excluded: chain e residue 690 GLN Chi-restraints excluded: chain e residue 702 THR Chi-restraints excluded: chain e residue 877 LEU Chi-restraints excluded: chain e residue 902 TRP Chi-restraints excluded: chain e residue 905 GLU Chi-restraints excluded: chain e residue 937 PHE Chi-restraints excluded: chain e residue 1001 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 54 THR Chi-restraints excluded: chain f residue 179 MET Chi-restraints excluded: chain f residue 197 THR Chi-restraints excluded: chain f residue 199 MET Chi-restraints excluded: chain f residue 231 VAL Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 349 GLN Chi-restraints excluded: chain f residue 351 TYR Chi-restraints excluded: chain f residue 418 THR Chi-restraints excluded: chain f residue 429 LYS Chi-restraints excluded: chain f residue 546 ASP Chi-restraints excluded: chain f residue 562 ASN Chi-restraints excluded: chain f residue 587 MET Chi-restraints excluded: chain f residue 627 MET Chi-restraints excluded: chain g residue 31 LYS Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 151 ASP Chi-restraints excluded: chain g residue 227 SER Chi-restraints excluded: chain g residue 279 LEU Chi-restraints excluded: chain g residue 416 MET Chi-restraints excluded: chain g residue 452 CYS Chi-restraints excluded: chain g residue 467 MET Chi-restraints excluded: chain g residue 536 MET Chi-restraints excluded: chain g residue 556 GLU Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 604 LEU Chi-restraints excluded: chain g residue 649 ILE Chi-restraints excluded: chain g residue 699 THR Chi-restraints excluded: chain g residue 809 SER Chi-restraints excluded: chain g residue 837 HIS Chi-restraints excluded: chain g residue 924 THR Chi-restraints excluded: chain g residue 935 TYR Chi-restraints excluded: chain h residue 213 TYR Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 290 SER Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain h residue 363 LEU Chi-restraints excluded: chain h residue 403 PHE Chi-restraints excluded: chain h residue 535 MET Chi-restraints excluded: chain h residue 612 LEU Chi-restraints excluded: chain h residue 667 MET Chi-restraints excluded: chain h residue 683 PHE Chi-restraints excluded: chain h residue 753 TYR Chi-restraints excluded: chain h residue 774 LEU Chi-restraints excluded: chain h residue 822 VAL Chi-restraints excluded: chain h residue 876 TYR Chi-restraints excluded: chain h residue 889 SER Chi-restraints excluded: chain h residue 896 GLN Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 182 TYR Chi-restraints excluded: chain i residue 527 VAL Chi-restraints excluded: chain i residue 601 HIS Chi-restraints excluded: chain k residue 142 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain k residue 372 MET Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 437 MET Chi-restraints excluded: chain k residue 518 HIS Chi-restraints excluded: chain m residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 696 optimal weight: 5.9990 chunk 933 optimal weight: 0.4980 chunk 268 optimal weight: 0.9980 chunk 808 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 878 optimal weight: 6.9990 chunk 367 optimal weight: 0.5980 chunk 901 optimal weight: 0.7980 chunk 111 optimal weight: 30.0000 chunk 161 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 399 GLN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 63 HIS ** q 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 272 GLN q 288 GLN ** a1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1380 GLN a1893 HIS a2087 ASN a2160 HIS ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 534 HIS ** b 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 176 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 810 HIS d 918 ASN ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN g 399 GLN ** g 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 715 HIS ** g 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 792 GLN g 885 ASN h 388 ASN ** h 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 795 HIS ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 288 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.113096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.098974 restraints weight = 526446.675| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 5.47 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.9978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 79542 Z= 0.245 Angle : 0.744 19.471 108531 Z= 0.368 Chirality : 0.045 0.769 13163 Planarity : 0.005 0.113 14182 Dihedral : 4.726 70.402 11625 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 1.49 % Allowed : 23.91 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -0.06 (0.08), residues: 10951 helix: 0.74 (0.07), residues: 6531 sheet: -1.19 (0.23), residues: 469 loop : -1.12 (0.10), residues: 3951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP b 337 HIS 0.022 0.001 HIS b 534 PHE 0.061 0.002 PHE e 931 TYR 0.057 0.002 TYR g 752 ARG 0.020 0.001 ARG b 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19309.61 seconds wall clock time: 340 minutes 4.33 seconds (20404.33 seconds total)