Starting phenix.real_space_refine on Sat Mar 23 06:33:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tub_26131/03_2024/7tub_26131_updated.pdb" } resolution = 3.6 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= 1.000 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 220 5.16 5 C 22426 2.51 5 N 6233 2.21 5 O 6942 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "G ASP 358": "OD1" <-> "OD2" Residue "G ASP 382": "OD1" <-> "OD2" Residue "G GLU 389": "OE1" <-> "OE2" Residue "G ASP 529": "OD1" <-> "OD2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "I GLU 238": "OE1" <-> "OE2" Residue "I TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 298": "OD1" <-> "OD2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I ASP 496": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3442 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4056 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 14, 'TRANS': 514} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 17.73, per 1000 atoms: 0.49 Number of scatterers: 35877 At special positions: 0 Unit cell: (180.4, 183.7, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 220 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6942 8.00 N 6233 7.00 C 22426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM35700 O3A ADP D 602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 7.0 seconds 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8658 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 52 sheets defined 49.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.80 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.712A pdb=" N ASN A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 109 through 126 removed outlier: 4.024A pdb=" N VAL A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 120 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 125 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.691A pdb=" N LEU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 194 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.215A pdb=" N CYS A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 removed outlier: 3.605A pdb=" N HIS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.571A pdb=" N GLN A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.656A pdb=" N ASP A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 374 through 389 removed outlier: 4.072A pdb=" N LYS A 379 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.511A pdb=" N GLU A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.693A pdb=" N ALA A 411 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 419 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 24 through 46 removed outlier: 4.248A pdb=" N TYR B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 121 removed outlier: 4.201A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.926A pdb=" N SER B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 262 through 286 removed outlier: 4.779A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 382 through 404 Processing helix chain 'B' and resid 414 through 429 removed outlier: 4.039A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.786A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.753A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 519 removed outlier: 3.557A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 35 removed outlier: 3.682A pdb=" N GLN C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.558A pdb=" N ALA C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.715A pdb=" N VAL C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 118 through 139 removed outlier: 3.734A pdb=" N GLN C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 163 removed outlier: 3.522A pdb=" N ARG C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 184 removed outlier: 5.608A pdb=" N ALA C 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP C 181 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 184 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.512A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 316 through 326 Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.584A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.509A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 443 removed outlier: 4.141A pdb=" N LEU C 434 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 435 " --> pdb=" O GLN C 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 442 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 443 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 506 through 524 removed outlier: 3.623A pdb=" N ALA C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.994A pdb=" N LYS D 35 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D 39 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 47 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.134A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 removed outlier: 3.510A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 175 removed outlier: 4.582A pdb=" N SER D 175 " --> pdb=" O THR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.706A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG D 183 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET D 185 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN D 191 " --> pdb=" O ILE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 271 through 295 removed outlier: 3.537A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 289 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.522A pdb=" N HIS D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 392 through 414 Processing helix chain 'D' and resid 424 through 438 removed outlier: 3.775A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 455 Processing helix chain 'D' and resid 457 through 466 removed outlier: 3.517A pdb=" N ASN D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 483 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 510 through 527 removed outlier: 3.712A pdb=" N MET D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 42 removed outlier: 3.593A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.763A pdb=" N LEU E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.915A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 119 removed outlier: 3.738A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 144 removed outlier: 3.519A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 166 Processing helix chain 'E' and resid 171 through 190 removed outlier: 3.751A pdb=" N LYS E 176 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP E 177 " --> pdb=" O HIS E 174 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR E 180 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 182 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 184 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 185 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 186 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 262 through 285 removed outlier: 3.639A pdb=" N LYS E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 307 removed outlier: 3.606A pdb=" N GLN E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 327 removed outlier: 3.653A pdb=" N LEU E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 402 removed outlier: 3.672A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 425 removed outlier: 3.520A pdb=" N LEU E 416 " --> pdb=" O CYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 454 removed outlier: 3.541A pdb=" N LEU E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 444 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Proline residue: E 447 - end of helix removed outlier: 3.516A pdb=" N ASN E 453 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 515 removed outlier: 3.603A pdb=" N ALA E 511 " --> pdb=" O ALA E 507 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 512 " --> pdb=" O ALA E 508 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 47 removed outlier: 3.571A pdb=" N PHE F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 80 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 91 through 101 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.792A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 151 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 175 through 192 removed outlier: 4.538A pdb=" N GLN F 178 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER F 181 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 183 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER F 184 " --> pdb=" O SER F 181 " (cutoff:3.500A) Proline residue: F 185 - end of helix removed outlier: 3.798A pdb=" N VAL F 188 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 269 through 293 removed outlier: 4.420A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 333 through 340 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 353 through 355 No H-bonds generated for 'chain 'F' and resid 353 through 355' Processing helix chain 'F' and resid 395 through 417 Processing helix chain 'F' and resid 427 through 442 removed outlier: 3.583A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 468 removed outlier: 3.725A pdb=" N MET F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL F 460 " --> pdb=" O ASP F 456 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Proline residue: F 462 - end of helix Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 504 through 506 No H-bonds generated for 'chain 'F' and resid 504 through 506' Processing helix chain 'F' and resid 512 through 531 removed outlier: 4.119A pdb=" N LYS F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 35 removed outlier: 3.600A pdb=" N ARG G 18 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER G 19 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN G 20 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET G 23 " --> pdb=" O GLN G 20 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 27 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS G 33 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER G 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'G' and resid 70 through 85 removed outlier: 4.424A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 109 removed outlier: 4.094A pdb=" N VAL G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 133 removed outlier: 3.692A pdb=" N ASN G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 156 removed outlier: 3.510A pdb=" N LEU G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.556A pdb=" N ILE G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 257 through 281 removed outlier: 4.345A pdb=" N ASP G 261 " --> pdb=" O GLU G 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 262 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN G 265 " --> pdb=" O GLN G 262 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE G 270 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR G 271 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 280 " --> pdb=" O LYS G 277 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 303 removed outlier: 3.942A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 323 Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 382 through 404 removed outlier: 3.573A pdb=" N MET G 388 " --> pdb=" O MET G 384 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 429 removed outlier: 4.226A pdb=" N THR G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER G 429 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.827A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL G 447 " --> pdb=" O ARG G 443 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE G 448 " --> pdb=" O SER G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 460 through 475 removed outlier: 3.677A pdb=" N VAL G 464 " --> pdb=" O SER G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 484 removed outlier: 4.615A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 501 No H-bonds generated for 'chain 'G' and resid 498 through 501' Processing helix chain 'G' and resid 507 through 526 removed outlier: 3.583A pdb=" N ILE G 524 " --> pdb=" O ALA G 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.617A pdb=" N ILE H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.624A pdb=" N LEU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.707A pdb=" N SER H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 110 through 115 removed outlier: 3.742A pdb=" N GLN H 115 " --> pdb=" O HIS H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 139 removed outlier: 3.851A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 160 removed outlier: 3.628A pdb=" N ASN H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 183 removed outlier: 3.810A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER H 170 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS H 173 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 176 " --> pdb=" O CYS H 173 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP H 178 " --> pdb=" O ILE H 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 179 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 180 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL H 183 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'H' and resid 261 through 285 removed outlier: 4.624A pdb=" N THR H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU H 285 " --> pdb=" O ASP H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 307 Processing helix chain 'H' and resid 317 through 327 removed outlier: 3.519A pdb=" N ASN H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG H 322 " --> pdb=" O THR H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 337 No H-bonds generated for 'chain 'H' and resid 335 through 337' Processing helix chain 'H' and resid 381 through 403 removed outlier: 3.532A pdb=" N ASP H 393 " --> pdb=" O ARG H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 428 removed outlier: 3.847A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA H 428 " --> pdb=" O GLU H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 455 Proline residue: H 436 - end of helix removed outlier: 4.324A pdb=" N VAL H 440 " --> pdb=" O TYR H 437 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 446 " --> pdb=" O ALA H 443 " (cutoff:3.500A) Proline residue: H 448 - end of helix removed outlier: 3.585A pdb=" N ASN H 454 " --> pdb=" O LEU H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 471 Processing helix chain 'H' and resid 490 through 493 No H-bonds generated for 'chain 'H' and resid 490 through 493' Processing helix chain 'H' and resid 499 through 518 removed outlier: 3.593A pdb=" N ARG H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.575A pdb=" N GLY I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 73 through 88 removed outlier: 3.857A pdb=" N ILE I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR I 88 " --> pdb=" O GLN I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.718A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 removed outlier: 3.530A pdb=" N GLU I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 137 " --> pdb=" O PHE I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 Processing helix chain 'I' and resid 162 through 179 removed outlier: 3.601A pdb=" N ASP I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'I' and resid 253 through 281 removed outlier: 4.255A pdb=" N ARG I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE I 266 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 308 removed outlier: 3.930A pdb=" N GLU I 308 " --> pdb=" O ALA I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 327 removed outlier: 3.650A pdb=" N ARG I 323 " --> pdb=" O ASN I 320 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU I 324 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 343 No H-bonds generated for 'chain 'I' and resid 341 through 343' Processing helix chain 'I' and resid 381 through 403 Processing helix chain 'I' and resid 413 through 426 removed outlier: 3.557A pdb=" N LYS I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 426 " --> pdb=" O LEU I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 455 removed outlier: 3.865A pdb=" N GLN I 434 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU I 444 " --> pdb=" O ALA I 441 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE I 447 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Proline residue: I 448 - end of helix removed outlier: 3.531A pdb=" N LEU I 451 " --> pdb=" O PRO I 448 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN I 454 " --> pdb=" O LEU I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 468 Processing helix chain 'I' and resid 489 through 492 No H-bonds generated for 'chain 'I' and resid 489 through 492' Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.554A pdb=" N THR I 509 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 removed outlier: 8.264A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY A 132 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE A 7 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 134 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA A 9 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 136 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 165 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS A 137 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 167 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU A 198 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N SER A 168 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR A 200 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 170 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 202 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ASP A 203 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 265 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER A 371 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 364 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 312 " --> pdb=" O ASN A 370 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 350 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE A 317 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA A 352 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= D, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= E, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.825A pdb=" N SER B 373 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS B 205 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 375 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE B 207 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU B 377 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 223 Processing sheet with id= G, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.643A pdb=" N VAL B 290 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR B 242 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 292 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET B 311 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR B 293 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 313 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 498 through 500 removed outlier: 3.771A pdb=" N CYS B 149 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL B 147 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 478 through 480 Processing sheet with id= J, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= K, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= L, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.693A pdb=" N CYS C 370 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LYS C 198 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE C 372 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL C 200 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU C 374 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 213 through 217 Processing sheet with id= N, first strand: chain 'C' and resid 237 through 240 removed outlier: 6.585A pdb=" N VAL C 288 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU C 240 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 290 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE C 309 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N SER C 291 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA C 311 " --> pdb=" O SER C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= P, first strand: chain 'C' and resid 485 through 488 Processing sheet with id= Q, first strand: chain 'D' and resid 25 through 29 removed outlier: 3.575A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 28 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.908A pdb=" N VAL D 383 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU D 212 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE D 385 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= U, first strand: chain 'D' and resid 354 through 356 removed outlier: 6.519A pdb=" N LEU D 299 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= W, first strand: chain 'E' and resid 50 through 53 Processing sheet with id= X, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.789A pdb=" N CYS E 371 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 202 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE E 373 " --> pdb=" O ILE E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 218 through 220 Processing sheet with id= Z, first strand: chain 'E' and resid 344 through 346 removed outlier: 3.567A pdb=" N ILE E 237 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS E 289 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA E 240 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 291 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET E 310 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN E 292 " --> pdb=" O MET E 310 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE E 312 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 406 through 408 Processing sheet with id= AB, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.515A pdb=" N THR E 484 " --> pdb=" O ASP E 479 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= AD, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.959A pdb=" N VAL F 386 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL F 211 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE F 388 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 222 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 226 through 229 Processing sheet with id= AF, first strand: chain 'F' and resid 357 through 359 removed outlier: 6.496A pdb=" N VAL F 297 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET F 323 " --> pdb=" O LEU F 298 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 421 through 423 Processing sheet with id= AH, first strand: chain 'F' and resid 491 through 494 Processing sheet with id= AI, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= AJ, first strand: chain 'G' and resid 180 through 182 Processing sheet with id= AK, first strand: chain 'G' and resid 196 through 199 removed outlier: 4.036A pdb=" N ASN G 196 " --> pdb=" O ALA G 373 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.595A pdb=" N ASP G 359 " --> pdb=" O ILE G 356 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 346 through 348 removed outlier: 6.558A pdb=" N VAL G 285 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU G 237 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU G 287 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET G 306 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR G 288 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL G 308 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 408 through 410 Processing sheet with id= AO, first strand: chain 'H' and resid 15 through 18 removed outlier: 3.649A pdb=" N SER H 524 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 48 through 51 Processing sheet with id= AQ, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.711A pdb=" N CYS H 372 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU H 202 " --> pdb=" O CYS H 372 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE H 374 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE H 204 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU H 376 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 215 " --> pdb=" O THR H 373 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 218 through 220 removed outlier: 3.608A pdb=" N THR H 364 " --> pdb=" O LEU H 349 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 349 " --> pdb=" O THR H 364 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 238 through 240 removed outlier: 6.567A pdb=" N VAL H 289 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR H 310 " --> pdb=" O VAL H 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'H' and resid 407 through 409 Processing sheet with id= AU, first strand: chain 'H' and resid 478 through 480 Processing sheet with id= AV, first strand: chain 'I' and resid 12 through 14 Processing sheet with id= AW, first strand: chain 'I' and resid 191 through 196 removed outlier: 7.175A pdb=" N VAL I 372 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N MET I 194 " --> pdb=" O VAL I 372 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU I 374 " --> pdb=" O MET I 194 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET I 196 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE I 376 " --> pdb=" O MET I 196 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 210 through 212 Processing sheet with id= AY, first strand: chain 'I' and resid 345 through 347 removed outlier: 6.918A pdb=" N GLY I 288 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU I 231 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL I 290 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS I 233 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE I 292 " --> pdb=" O CYS I 233 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL I 311 " --> pdb=" O VAL I 291 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN I 293 " --> pdb=" O VAL I 311 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU I 313 " --> pdb=" O ASN I 293 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'I' and resid 477 through 479 1614 hydrogen bonds defined for protein. 4179 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: 12.47 Time building geometry restraints manager: 14.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6246 1.29 - 1.42: 7856 1.42 - 1.56: 21801 1.56 - 1.69: 34 1.69 - 1.82: 379 Bond restraints: 36316 Sorted by residual: bond pdb=" F3 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F2 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F3 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F1 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F2 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 36311 not shown) Histogram of bond angle deviations from ideal: 98.75 - 106.30: 838 106.30 - 113.86: 21631 113.86 - 121.41: 17886 121.41 - 128.97: 8541 128.97 - 136.53: 161 Bond angle restraints: 49057 Sorted by residual: angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 110.62 100.96 9.66 1.02e+00 9.61e-01 8.98e+01 angle pdb=" CA HIS I 198 " pdb=" CB HIS I 198 " pdb=" CG HIS I 198 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.84e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.50 122.02 -9.52 1.16e+00 7.43e-01 6.74e+01 angle pdb=" CA ASP B 193 " pdb=" C ASP B 193 " pdb=" O ASP B 193 " ideal model delta sigma weight residual 120.54 111.61 8.93 1.13e+00 7.83e-01 6.24e+01 angle pdb=" N LYS A 174 " pdb=" CA LYS A 174 " pdb=" C LYS A 174 " ideal model delta sigma weight residual 111.28 103.29 7.99 1.09e+00 8.42e-01 5.37e+01 ... (remaining 49052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 21803 35.86 - 71.72: 534 71.72 - 107.58: 48 107.58 - 143.43: 5 143.43 - 179.29: 2 Dihedral angle restraints: 22392 sinusoidal: 9013 harmonic: 13379 Sorted by residual: dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual 300.00 120.71 179.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual 300.00 145.66 154.35 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP G 602 " pdb=" O3A ADP G 602 " pdb=" PA ADP G 602 " pdb=" PB ADP G 602 " ideal model delta sinusoidal sigma weight residual 300.00 158.41 141.59 1 2.00e+01 2.50e-03 4.28e+01 ... (remaining 22389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5085 0.064 - 0.127: 670 0.127 - 0.191: 40 0.191 - 0.255: 7 0.255 - 0.318: 4 Chirality restraints: 5806 Sorted by residual: chirality pdb=" CA HIS F 406 " pdb=" N HIS F 406 " pdb=" C HIS F 406 " pdb=" CB HIS F 406 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA SER B 189 " pdb=" N SER B 189 " pdb=" C SER B 189 " pdb=" CB SER B 189 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 5803 not shown) Planarity restraints: 6282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 171 " 0.028 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C PRO A 171 " -0.097 2.00e-02 2.50e+03 pdb=" O PRO A 171 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 172 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 188 " -0.022 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C VAL B 188 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL B 188 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 189 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS I 198 " 0.019 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C HIS I 198 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS I 198 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS I 199 " 0.024 2.00e-02 2.50e+03 ... (remaining 6279 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 119 2.42 - 3.04: 21324 3.04 - 3.66: 51048 3.66 - 4.28: 74653 4.28 - 4.90: 126097 Nonbonded interactions: 273241 Sorted by model distance: nonbonded pdb="MG MG G 601 " pdb="AL AF3 G 603 " model vdw 1.797 1.890 nonbonded pdb="MG MG D 601 " pdb="AL AF3 D 603 " model vdw 1.816 1.890 nonbonded pdb="MG MG D 601 " pdb=" F1 AF3 D 603 " model vdw 1.891 2.120 nonbonded pdb="MG MG G 601 " pdb=" O3B ADP G 602 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP B 99 " pdb="MG MG B 601 " model vdw 1.903 2.170 ... (remaining 273236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.070 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 92.450 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 0.164 36316 Z= 0.356 Angle : 0.701 13.083 49057 Z= 0.408 Chirality : 0.044 0.318 5806 Planarity : 0.004 0.099 6282 Dihedral : 15.999 179.293 13734 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 0.49 % Allowed : 12.66 % Favored : 86.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4628 helix: -0.30 (0.11), residues: 2244 sheet: 0.02 (0.21), residues: 653 loop : -1.19 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.018 0.001 HIS I 198 PHE 0.012 0.001 PHE I 123 TYR 0.016 0.001 TYR A 425 ARG 0.006 0.000 ARG E 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 4.045 Fit side-chains REVERT: D 239 MET cc_start: 0.8928 (mtt) cc_final: 0.8435 (mtt) REVERT: F 407 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7768 (p0) outliers start: 19 outliers final: 6 residues processed: 243 average time/residue: 0.4356 time to fit residues: 181.3584 Evaluate side-chains 222 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 219 optimal weight: 8.9990 chunk 268 optimal weight: 4.9990 chunk 417 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 GLN I 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36316 Z= 0.221 Angle : 0.595 9.272 49057 Z= 0.301 Chirality : 0.044 0.173 5806 Planarity : 0.004 0.072 6282 Dihedral : 7.703 168.350 5052 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.57 % Allowed : 13.41 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.12), residues: 4628 helix: 0.74 (0.11), residues: 2229 sheet: 0.18 (0.22), residues: 616 loop : -1.15 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.008 0.001 HIS I 198 PHE 0.013 0.001 PHE B 103 TYR 0.015 0.001 TYR C 438 ARG 0.005 0.000 ARG E 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 3.923 Fit side-chains REVERT: A 226 ASN cc_start: 0.7890 (m110) cc_final: 0.7688 (m110) REVERT: A 341 PHE cc_start: 0.3469 (OUTLIER) cc_final: 0.3126 (t80) REVERT: C 414 MET cc_start: 0.8039 (mmt) cc_final: 0.7785 (mmt) REVERT: F 407 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7838 (m-30) outliers start: 61 outliers final: 24 residues processed: 294 average time/residue: 0.4129 time to fit residues: 210.1409 Evaluate side-chains 249 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 418 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 372 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN C 511 ASN D 298 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN I 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36316 Z= 0.181 Angle : 0.541 9.198 49057 Z= 0.267 Chirality : 0.042 0.187 5806 Planarity : 0.003 0.062 6282 Dihedral : 6.949 149.133 5041 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.52 % Allowed : 14.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4628 helix: 1.14 (0.11), residues: 2245 sheet: 0.26 (0.21), residues: 636 loop : -1.10 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 484 HIS 0.004 0.001 HIS B 365 PHE 0.016 0.001 PHE E 252 TYR 0.016 0.001 TYR F 269 ARG 0.003 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 246 time to evaluate : 4.176 Fit side-chains revert: symmetry clash REVERT: A 226 ASN cc_start: 0.7889 (m110) cc_final: 0.7615 (m110) REVERT: A 341 PHE cc_start: 0.3596 (OUTLIER) cc_final: 0.3332 (t80) REVERT: C 414 MET cc_start: 0.8020 (mmt) cc_final: 0.7746 (mmt) REVERT: F 60 MET cc_start: 0.8111 (ttm) cc_final: 0.7770 (ttm) REVERT: F 407 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: I 64 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8807 (mm) outliers start: 59 outliers final: 24 residues processed: 290 average time/residue: 0.4120 time to fit residues: 207.2806 Evaluate side-chains 252 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 199 optimal weight: 0.0170 chunk 281 optimal weight: 3.9990 chunk 419 optimal weight: 9.9990 chunk 444 optimal weight: 0.0040 chunk 219 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 383 ASN F 72 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36316 Z= 0.303 Angle : 0.597 8.365 49057 Z= 0.294 Chirality : 0.044 0.208 5806 Planarity : 0.004 0.060 6282 Dihedral : 6.896 131.974 5037 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 2.42 % Allowed : 15.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 4628 helix: 1.12 (0.11), residues: 2236 sheet: 0.04 (0.21), residues: 631 loop : -1.14 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.005 0.001 HIS H 526 PHE 0.016 0.001 PHE G 167 TYR 0.015 0.001 TYR A 159 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 230 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 226 ASN cc_start: 0.8057 (m110) cc_final: 0.7828 (m-40) REVERT: A 341 PHE cc_start: 0.3693 (OUTLIER) cc_final: 0.3411 (t80) REVERT: B 208 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (tt) REVERT: C 414 MET cc_start: 0.8112 (mmt) cc_final: 0.7765 (mmt) REVERT: D 456 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: D 526 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8083 (ttt) REVERT: E 531 ASP cc_start: 0.6305 (OUTLIER) cc_final: 0.5953 (m-30) REVERT: F 60 MET cc_start: 0.8172 (ttm) cc_final: 0.7876 (ttm) REVERT: F 407 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: I 64 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8861 (mm) REVERT: I 112 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6708 (mp0) outliers start: 94 outliers final: 51 residues processed: 306 average time/residue: 0.4236 time to fit residues: 225.8848 Evaluate side-chains 287 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 227 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 366 CYS Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 331 optimal weight: 0.4980 chunk 183 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 307 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 399 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN C 60 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36316 Z= 0.157 Angle : 0.528 8.328 49057 Z= 0.257 Chirality : 0.042 0.235 5806 Planarity : 0.003 0.055 6282 Dihedral : 6.559 129.865 5037 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 16.50 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 4628 helix: 1.33 (0.11), residues: 2247 sheet: 0.21 (0.21), residues: 625 loop : -1.02 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 101 HIS 0.003 0.001 HIS H 526 PHE 0.010 0.001 PHE G 167 TYR 0.014 0.001 TYR F 269 ARG 0.006 0.000 ARG H 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 248 time to evaluate : 4.158 Fit side-chains revert: symmetry clash REVERT: A 226 ASN cc_start: 0.7971 (m110) cc_final: 0.7678 (m-40) REVERT: B 208 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt) REVERT: B 249 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: C 45 MET cc_start: 0.8061 (mmt) cc_final: 0.7688 (mmt) REVERT: D 526 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7916 (ttt) REVERT: E 531 ASP cc_start: 0.6240 (OUTLIER) cc_final: 0.5916 (m-30) REVERT: F 407 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: I 64 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8824 (mm) outliers start: 83 outliers final: 44 residues processed: 316 average time/residue: 0.4059 time to fit residues: 222.4193 Evaluate side-chains 285 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 235 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 445 optimal weight: 0.9990 chunk 369 optimal weight: 0.5980 chunk 206 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 36316 Z= 0.154 Angle : 0.522 9.110 49057 Z= 0.251 Chirality : 0.041 0.228 5806 Planarity : 0.003 0.051 6282 Dihedral : 6.391 129.347 5037 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 1.75 % Allowed : 17.01 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4628 helix: 1.47 (0.11), residues: 2250 sheet: 0.29 (0.22), residues: 624 loop : -0.95 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 101 HIS 0.003 0.001 HIS B 365 PHE 0.010 0.001 PHE G 167 TYR 0.012 0.001 TYR F 269 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 249 time to evaluate : 4.413 Fit side-chains revert: symmetry clash REVERT: A 226 ASN cc_start: 0.7991 (m110) cc_final: 0.7665 (m-40) REVERT: A 324 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7362 (mttt) REVERT: B 85 MET cc_start: 0.8493 (mmm) cc_final: 0.8233 (mmm) REVERT: B 208 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 249 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7141 (mpp) REVERT: C 45 MET cc_start: 0.8260 (mmt) cc_final: 0.7912 (mmt) REVERT: D 456 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: D 526 MET cc_start: 0.8210 (ttt) cc_final: 0.7989 (ttt) REVERT: E 531 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5912 (m-30) REVERT: F 407 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: G 44 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7943 (mpp) REVERT: I 64 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8863 (mm) outliers start: 68 outliers final: 47 residues processed: 303 average time/residue: 0.4453 time to fit residues: 235.1472 Evaluate side-chains 291 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 325 optimal weight: 0.1980 chunk 251 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 443 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN G 30 ASN H 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36316 Z= 0.287 Angle : 0.580 9.634 49057 Z= 0.282 Chirality : 0.044 0.238 5806 Planarity : 0.003 0.053 6282 Dihedral : 6.532 131.267 5037 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 2.16 % Allowed : 17.47 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4628 helix: 1.36 (0.11), residues: 2247 sheet: 0.15 (0.21), residues: 625 loop : -1.00 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.005 0.001 HIS H 526 PHE 0.015 0.001 PHE G 167 TYR 0.014 0.001 TYR A 159 ARG 0.006 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 238 time to evaluate : 4.716 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6755 (tmm) cc_final: 0.6442 (tmm) REVERT: A 226 ASN cc_start: 0.8052 (m110) cc_final: 0.7728 (m-40) REVERT: A 324 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7374 (mttt) REVERT: B 208 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8555 (tt) REVERT: B 249 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6878 (mpp) REVERT: D 456 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: D 526 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7974 (ttt) REVERT: E 531 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5946 (m-30) REVERT: F 407 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: G 44 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (mpp) REVERT: G 313 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7973 (tptm) REVERT: I 64 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8887 (mm) outliers start: 84 outliers final: 62 residues processed: 305 average time/residue: 0.4121 time to fit residues: 217.3731 Evaluate side-chains 306 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 235 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 382 ASP Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36316 Z= 0.158 Angle : 0.530 10.753 49057 Z= 0.255 Chirality : 0.042 0.225 5806 Planarity : 0.003 0.051 6282 Dihedral : 6.376 131.077 5037 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 1.93 % Allowed : 17.83 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4628 helix: 1.51 (0.11), residues: 2250 sheet: 0.26 (0.22), residues: 614 loop : -0.91 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.003 0.001 HIS H 526 PHE 0.011 0.001 PHE G 167 TYR 0.011 0.001 TYR F 269 ARG 0.002 0.000 ARG E 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 243 time to evaluate : 4.301 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6665 (tmm) cc_final: 0.6374 (tmm) REVERT: A 226 ASN cc_start: 0.7995 (m110) cc_final: 0.7676 (m-40) REVERT: A 324 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7345 (mttt) REVERT: B 85 MET cc_start: 0.8512 (mmm) cc_final: 0.8242 (mmm) REVERT: B 88 MET cc_start: 0.7817 (mtp) cc_final: 0.7584 (mtt) REVERT: B 208 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 249 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7208 (mpp) REVERT: D 456 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: E 531 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5862 (m-30) REVERT: F 407 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: G 44 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: I 64 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 112 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6575 (mp0) outliers start: 75 outliers final: 61 residues processed: 307 average time/residue: 0.4115 time to fit residues: 218.2905 Evaluate side-chains 306 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 237 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 382 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 413 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 373 optimal weight: 4.9990 chunk 390 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36316 Z= 0.289 Angle : 0.593 11.881 49057 Z= 0.288 Chirality : 0.044 0.257 5806 Planarity : 0.003 0.053 6282 Dihedral : 6.488 130.947 5037 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 2.26 % Allowed : 17.65 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4628 helix: 1.39 (0.11), residues: 2238 sheet: 0.13 (0.21), residues: 636 loop : -0.99 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 304 HIS 0.005 0.001 HIS H 526 PHE 0.015 0.001 PHE G 167 TYR 0.014 0.001 TYR A 159 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 237 time to evaluate : 4.550 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6690 (tmm) cc_final: 0.6327 (tmm) REVERT: A 226 ASN cc_start: 0.8070 (m110) cc_final: 0.7738 (m-40) REVERT: A 324 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7534 (tppt) REVERT: B 208 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8567 (tt) REVERT: B 249 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6880 (mpp) REVERT: D 239 MET cc_start: 0.8833 (mtt) cc_final: 0.8327 (mtt) REVERT: D 456 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: D 526 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7971 (ttt) REVERT: E 302 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: E 531 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5896 (m-30) REVERT: F 407 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: G 44 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: G 313 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8001 (tptm) REVERT: I 64 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8884 (mm) REVERT: I 112 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6590 (mp0) outliers start: 88 outliers final: 66 residues processed: 311 average time/residue: 0.4445 time to fit residues: 239.8786 Evaluate side-chains 311 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 234 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 382 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 458 optimal weight: 0.9990 chunk 421 optimal weight: 8.9990 chunk 364 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 281 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36316 Z= 0.216 Angle : 0.562 12.627 49057 Z= 0.272 Chirality : 0.043 0.224 5806 Planarity : 0.003 0.053 6282 Dihedral : 6.417 130.600 5037 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.03 % Allowed : 17.96 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 4628 helix: 1.42 (0.11), residues: 2248 sheet: 0.17 (0.22), residues: 614 loop : -0.97 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.004 0.001 HIS H 526 PHE 0.013 0.001 PHE G 167 TYR 0.012 0.001 TYR A 159 ARG 0.003 0.000 ARG C 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 238 time to evaluate : 4.205 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6656 (tmm) cc_final: 0.6306 (tmm) REVERT: A 226 ASN cc_start: 0.8028 (m110) cc_final: 0.7695 (m-40) REVERT: A 324 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7525 (tppt) REVERT: B 208 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 249 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6921 (mpp) REVERT: D 239 MET cc_start: 0.8850 (mtt) cc_final: 0.8351 (mtt) REVERT: D 456 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: E 531 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5917 (m-30) REVERT: F 407 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: G 44 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: G 313 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7984 (tptm) REVERT: I 64 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (mm) REVERT: I 112 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6571 (mp0) outliers start: 79 outliers final: 67 residues processed: 305 average time/residue: 0.4215 time to fit residues: 220.9729 Evaluate side-chains 311 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 235 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 382 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 336 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 375 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074185 restraints weight = 81890.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076454 restraints weight = 40716.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077974 restraints weight = 24708.334| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36316 Z= 0.192 Angle : 0.553 12.573 49057 Z= 0.267 Chirality : 0.042 0.214 5806 Planarity : 0.003 0.052 6282 Dihedral : 6.334 130.689 5037 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.08 % Allowed : 17.94 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4628 helix: 1.49 (0.11), residues: 2245 sheet: 0.18 (0.22), residues: 614 loop : -0.91 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.004 0.001 HIS H 526 PHE 0.012 0.001 PHE G 167 TYR 0.012 0.001 TYR A 159 ARG 0.002 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5724.32 seconds wall clock time: 105 minutes 57.06 seconds (6357.06 seconds total)