Starting phenix.real_space_refine on Sun Dec 29 12:44:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644.map" model { file = "/net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ewf_28644/12_2024/8ewf_28644_trim.cif" } resolution = 3.92 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 220 5.16 5 C 18037 2.51 5 N 4984 2.21 5 O 5424 1.98 5 H 27869 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56534 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6564 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6490 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "E" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4192 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: G, K, O, I, M, Q Time building chain proxies: 26.66, per 1000 atoms: 0.47 Number of scatterers: 56534 At special positions: 0 Unit cell: (194.4, 159.6, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 O 5424 8.00 N 4984 7.00 C 18037 6.00 H 27869 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 28 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 266 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 396 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 280 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 141 " " NAG G 501 " - " ASN G 141 " " NAG K 501 " - " ASN K 141 " " NAG O 501 " - " ASN O 141 " Time building additional restraints: 12.13 Conformation dependent library (CDL) restraints added in 3.7 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6932 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 88 sheets defined 12.6% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.598A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 removed outlier: 4.277A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.955A pdb=" N SER A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.671A pdb=" N CYS C 225 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 401 Proline residue: C 399 - end of helix Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.729A pdb=" N VAL E 59 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.909A pdb=" N ALA E 163 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.875A pdb=" N ARG E 243 " --> pdb=" O PHE E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.599A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 259 removed outlier: 4.278A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 256 through 259' Processing helix chain 'G' and resid 404 through 414 removed outlier: 3.956A pdb=" N SER G 408 " --> pdb=" O THR G 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP G 409 " --> pdb=" O THR G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 434 Processing helix chain 'I' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS I 225 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR I 358 " --> pdb=" O GLU I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 401 Proline residue: I 399 - end of helix Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.599A pdb=" N TYR K 242 " --> pdb=" O SER K 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 256 through 259 removed outlier: 4.278A pdb=" N CYS K 259 " --> pdb=" O PRO K 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing helix chain 'K' and resid 404 through 414 removed outlier: 3.955A pdb=" N SER K 408 " --> pdb=" O THR K 404 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 434 Processing helix chain 'M' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 362 removed outlier: 3.916A pdb=" N TYR M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 401 Proline residue: M 399 - end of helix Processing helix chain 'M' and resid 411 through 416 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'O' and resid 238 through 246 removed outlier: 3.598A pdb=" N TYR O 242 " --> pdb=" O SER O 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS O 245 " --> pdb=" O LYS O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 4.277A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 404 through 414 removed outlier: 3.954A pdb=" N SER O 408 " --> pdb=" O THR O 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP O 409 " --> pdb=" O THR O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 434 Processing helix chain 'Q' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS Q 225 " --> pdb=" O ILE Q 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR Q 358 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 401 Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 411 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.593A pdb=" N MET A 31 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 134 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 35 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA9, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.620A pdb=" N VAL A 220 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 305 removed outlier: 4.109A pdb=" N MET A 299 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 319 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS A 301 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 303 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 18 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'C' and resid 66 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'C' and resid 149 through 156 Processing sheet with id=AB9, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AC1, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AC2, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS C 200 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 226 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 44 removed outlier: 4.835A pdb=" N LEU E 35 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL E 287 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER E 37 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 289 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER E 39 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN E 291 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 41 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR E 293 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU E 43 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG E 210 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG E 222 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AC6, first strand: chain 'E' and resid 99 through 100 removed outlier: 6.969A pdb=" N TRP E 74 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP E 91 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL E 72 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 93 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG E 70 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA E 173 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.592A pdb=" N MET G 31 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G 134 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AD2, first strand: chain 'G' and resid 44 through 48 Processing sheet with id=AD3, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD7, first strand: chain 'G' and resid 220 through 221 removed outlier: 3.619A pdb=" N VAL G 220 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 296 through 305 removed outlier: 4.108A pdb=" N MET G 299 " --> pdb=" O LYS G 319 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS G 319 " --> pdb=" O MET G 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS G 301 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE G 317 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL G 303 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL G 315 " --> pdb=" O VAL G 303 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AE1, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE2, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AE3, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AE4, first strand: chain 'I' and resid 66 through 71 Processing sheet with id=AE5, first strand: chain 'I' and resid 84 through 86 Processing sheet with id=AE6, first strand: chain 'I' and resid 149 through 156 Processing sheet with id=AE7, first strand: chain 'I' and resid 236 through 237 Processing sheet with id=AE8, first strand: chain 'I' and resid 183 through 184 Processing sheet with id=AE9, first strand: chain 'I' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS I 200 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS I 226 " --> pdb=" O LYS I 200 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'K' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.593A pdb=" N MET K 31 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU K 136 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU K 33 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG K 134 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER K 35 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 15 through 19 Processing sheet with id=AF5, first strand: chain 'K' and resid 44 through 48 Processing sheet with id=AF6, first strand: chain 'K' and resid 51 through 54 Processing sheet with id=AF7, first strand: chain 'K' and resid 51 through 54 Processing sheet with id=AF8, first strand: chain 'K' and resid 87 through 88 Processing sheet with id=AF9, first strand: chain 'K' and resid 203 through 205 Processing sheet with id=AG1, first strand: chain 'K' and resid 220 through 221 removed outlier: 3.619A pdb=" N VAL K 220 " --> pdb=" O SER K 234 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 296 through 305 removed outlier: 4.108A pdb=" N MET K 299 " --> pdb=" O LYS K 319 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS K 319 " --> pdb=" O MET K 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS K 301 " --> pdb=" O ILE K 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 317 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL K 303 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL K 315 " --> pdb=" O VAL K 303 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 343 through 346 Processing sheet with id=AG4, first strand: chain 'K' and resid 387 through 388 Processing sheet with id=AG5, first strand: chain 'M' and resid 17 through 18 Processing sheet with id=AG6, first strand: chain 'M' and resid 37 through 38 Processing sheet with id=AG7, first strand: chain 'M' and resid 66 through 71 Processing sheet with id=AG8, first strand: chain 'M' and resid 84 through 86 Processing sheet with id=AG9, first strand: chain 'M' and resid 149 through 156 Processing sheet with id=AH1, first strand: chain 'M' and resid 236 through 237 Processing sheet with id=AH2, first strand: chain 'M' and resid 183 through 184 Processing sheet with id=AH3, first strand: chain 'M' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS M 200 " --> pdb=" O HIS M 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS M 226 " --> pdb=" O LYS M 200 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AH6, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.592A pdb=" N MET O 31 " --> pdb=" O LEU O 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU O 136 " --> pdb=" O MET O 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU O 33 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG O 134 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER O 35 " --> pdb=" O LYS O 132 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 15 through 19 Processing sheet with id=AH8, first strand: chain 'O' and resid 44 through 48 Processing sheet with id=AH9, first strand: chain 'O' and resid 51 through 54 Processing sheet with id=AI1, first strand: chain 'O' and resid 51 through 54 Processing sheet with id=AI2, first strand: chain 'O' and resid 87 through 88 Processing sheet with id=AI3, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AI4, first strand: chain 'O' and resid 220 through 221 removed outlier: 3.620A pdb=" N VAL O 220 " --> pdb=" O SER O 234 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 296 through 305 removed outlier: 4.109A pdb=" N MET O 299 " --> pdb=" O LYS O 319 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS O 319 " --> pdb=" O MET O 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS O 301 " --> pdb=" O ILE O 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE O 317 " --> pdb=" O CYS O 301 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL O 303 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL O 315 " --> pdb=" O VAL O 303 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 343 through 346 Processing sheet with id=AI7, first strand: chain 'O' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'Q' and resid 17 through 18 Processing sheet with id=AI9, first strand: chain 'Q' and resid 37 through 38 Processing sheet with id=AJ1, first strand: chain 'Q' and resid 66 through 71 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 84 through 86 Processing sheet with id=AJ3, first strand: chain 'Q' and resid 149 through 156 Processing sheet with id=AJ4, first strand: chain 'Q' and resid 236 through 237 Processing sheet with id=AJ5, first strand: chain 'Q' and resid 183 through 184 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS Q 200 " --> pdb=" O HIS Q 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS Q 226 " --> pdb=" O LYS Q 200 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 275 through 279 1026 hydrogen bonds defined for protein. 2574 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: 22.82 Time building geometry restraints manager: 14.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 27852 1.04 - 1.24: 3984 1.24 - 1.45: 8754 1.45 - 1.65: 16374 1.65 - 1.86: 297 Bond restraints: 57261 Sorted by residual: bond pdb=" N SER E 32 " pdb=" H2 SER E 32 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N TYR O 1 " pdb=" H3 TYR O 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR G 1 " pdb=" H2 TYR G 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR K 1 " pdb=" H3 TYR K 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR A 1 " pdb=" H3 TYR A 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 57256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.63: 103448 10.63 - 21.27: 4 21.27 - 31.90: 1 31.90 - 42.54: 0 42.54 - 53.17: 1 Bond angle restraints: 103454 Sorted by residual: angle pdb=" H1 SER E 32 " pdb=" N SER E 32 " pdb=" H2 SER E 32 " ideal model delta sigma weight residual 109.47 56.30 53.17 3.00e+00 1.11e-01 3.14e+02 angle pdb=" H1 SER E 32 " pdb=" N SER E 32 " pdb=" H3 SER E 32 " ideal model delta sigma weight residual 109.47 136.51 -27.04 3.00e+00 1.11e-01 8.13e+01 angle pdb=" N GLY E 96 " pdb=" CA GLY E 96 " pdb=" C GLY E 96 " ideal model delta sigma weight residual 110.69 118.73 -8.04 2.05e+00 2.38e-01 1.54e+01 angle pdb=" H1 TYR G 1 " pdb=" N TYR G 1 " pdb=" H2 TYR G 1 " ideal model delta sigma weight residual 109.47 97.73 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" H1 TYR K 1 " pdb=" N TYR K 1 " pdb=" H2 TYR K 1 " ideal model delta sigma weight residual 109.47 97.77 11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 103449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 23789 17.80 - 35.61: 2745 35.61 - 53.41: 762 53.41 - 71.21: 195 71.21 - 89.01: 60 Dihedral angle restraints: 27551 sinusoidal: 14917 harmonic: 12634 Sorted by residual: dihedral pdb=" CB CYS C 153 " pdb=" SG CYS C 153 " pdb=" SG CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sinusoidal sigma weight residual -86.00 -164.47 78.47 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 170.79 -77.79 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -137.77 51.77 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 27548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2736 0.030 - 0.061: 1164 0.061 - 0.091: 349 0.091 - 0.121: 303 0.121 - 0.152: 22 Chirality restraints: 4574 Sorted by residual: chirality pdb=" CA ILE E 153 " pdb=" N ILE E 153 " pdb=" C ILE E 153 " pdb=" CB ILE E 153 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CB THR M 403 " pdb=" CA THR M 403 " pdb=" OG1 THR M 403 " pdb=" CG2 THR M 403 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CB THR Q 403 " pdb=" CA THR Q 403 " pdb=" OG1 THR Q 403 " pdb=" CG2 THR Q 403 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 4571 not shown) Planarity restraints: 8618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 141 " -0.030 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN K 141 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN K 141 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 141 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG K 501 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 339 " -0.021 2.00e-02 2.50e+03 1.12e-02 5.03e+00 pdb=" CG TRP C 339 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 339 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 339 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 339 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 339 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 339 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 339 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP C 339 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP C 339 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 339 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 339 " 0.020 2.00e-02 2.50e+03 1.12e-02 5.02e+00 pdb=" CG TRP Q 339 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 339 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 339 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 339 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 339 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 339 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 339 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 339 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP Q 339 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP Q 339 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP Q 339 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP Q 339 " -0.001 2.00e-02 2.50e+03 ... (remaining 8615 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 788 1.99 - 2.64: 79638 2.64 - 3.29: 170424 3.29 - 3.95: 215546 3.95 - 4.60: 316706 Nonbonded interactions: 783102 Sorted by model distance: nonbonded pdb=" O PRO C 20 " pdb="HH12 ARG I 144 " model vdw 1.337 2.450 nonbonded pdb=" O PRO I 20 " pdb="HH12 ARG M 144 " model vdw 1.386 2.450 nonbonded pdb=" O TYR K 390 " pdb=" HE1 TRP M 339 " model vdw 1.441 2.450 nonbonded pdb=" HZ1 LYS C 120 " pdb=" OD1 ASP E 97 " model vdw 1.485 2.450 nonbonded pdb="HH12 ARG C 144 " pdb=" O PRO M 20 " model vdw 1.502 2.450 ... (remaining 783097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = (chain 'C' and resid 5 through 423) selection = chain 'I' selection = (chain 'M' and resid 5 through 423) selection = (chain 'Q' and resid 5 through 423) } 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: 1.270 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: 0.810 Extract box with map and model: 1.670 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 103.270 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.004 0.048 29392 Z= 0.256 Angle : 0.684 8.863 40098 Z= 0.359 Chirality : 0.043 0.152 4574 Planarity : 0.005 0.058 5165 Dihedral : 16.919 89.015 10772 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.88 % Allowed : 35.98 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.26 (0.14), residues: 3679 helix: -1.58 (0.26), residues: 330 sheet: -0.26 (0.15), residues: 1193 loop : -1.03 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 339 HIS 0.009 0.001 HIS Q 142 PHE 0.026 0.002 PHE A 161 TYR 0.020 0.002 TYR M 237 ARG 0.012 0.001 ARG M 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 884 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 HIS cc_start: 0.3507 (OUTLIER) cc_final: 0.3058 (t70) REVERT: G 281 ASP cc_start: 0.8955 (t0) cc_final: 0.8733 (t0) REVERT: G 310 SER cc_start: 0.9320 (m) cc_final: 0.8867 (p) REVERT: G 351 GLN cc_start: 0.8275 (pp30) cc_final: 0.8008 (pp30) REVERT: I 45 THR cc_start: 0.9001 (m) cc_final: 0.8655 (p) REVERT: I 97 MET cc_start: 0.8681 (tpt) cc_final: 0.7791 (tpp) REVERT: I 305 ASN cc_start: 0.8257 (m-40) cc_final: 0.7987 (m-40) REVERT: I 332 ASN cc_start: 0.8720 (m-40) cc_final: 0.8101 (m-40) REVERT: I 338 TYR cc_start: 0.8321 (m-80) cc_final: 0.8082 (m-80) REVERT: I 341 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7824 (tt0) REVERT: K 85 TYR cc_start: 0.7118 (t80) cc_final: 0.6858 (t80) REVERT: K 162 VAL cc_start: 0.8451 (t) cc_final: 0.8231 (m) REVERT: K 165 PRO cc_start: 0.9350 (Cg_endo) cc_final: 0.9127 (Cg_exo) REVERT: K 217 THR cc_start: 0.8455 (p) cc_final: 0.8207 (p) REVERT: K 334 THR cc_start: 0.9269 (t) cc_final: 0.8721 (p) REVERT: K 375 HIS cc_start: 0.9197 (t-90) cc_final: 0.8734 (m-70) REVERT: M 45 THR cc_start: 0.9161 (m) cc_final: 0.8228 (p) REVERT: M 54 ILE cc_start: 0.9377 (tt) cc_final: 0.9157 (pt) REVERT: M 64 TRP cc_start: 0.8130 (p90) cc_final: 0.7916 (m-90) REVERT: M 70 MET cc_start: 0.6920 (tpp) cc_final: 0.6718 (tpp) REVERT: M 149 LYS cc_start: 0.9275 (ttmm) cc_final: 0.9041 (ttpp) REVERT: M 303 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8084 (tm-30) REVERT: M 356 ILE cc_start: 0.9212 (mm) cc_final: 0.9009 (tp) REVERT: O 29 LEU cc_start: 0.8989 (mm) cc_final: 0.8388 (mt) REVERT: O 46 TYR cc_start: 0.8799 (p90) cc_final: 0.8335 (p90) REVERT: O 123 ARG cc_start: 0.8980 (ttp-110) cc_final: 0.8737 (ttp-110) REVERT: O 199 GLN cc_start: 0.7472 (mp10) cc_final: 0.7224 (mp10) REVERT: O 310 SER cc_start: 0.9021 (m) cc_final: 0.8411 (t) REVERT: Q 45 THR cc_start: 0.9034 (m) cc_final: 0.8396 (p) REVERT: Q 149 LYS cc_start: 0.9306 (ttmm) cc_final: 0.9084 (ttpt) REVERT: Q 170 HIS cc_start: 0.7504 (p-80) cc_final: 0.7036 (p-80) REVERT: Q 171 MET cc_start: 0.8832 (ptm) cc_final: 0.8608 (pmm) REVERT: Q 245 ASN cc_start: 0.5732 (t0) cc_final: 0.4127 (t0) REVERT: Q 303 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8543 (tm-30) REVERT: Q 306 TYR cc_start: 0.8280 (t80) cc_final: 0.8067 (t80) REVERT: Q 307 HIS cc_start: 0.7532 (m90) cc_final: 0.6904 (m90) REVERT: Q 393 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8062 (mtt180) outliers start: 28 outliers final: 18 residues processed: 899 average time/residue: 0.7768 time to fit residues: 1073.3505 Evaluate side-chains 717 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 698 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 277 HIS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 260 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS C 245 ASN C 273 ASN E 189 ASN E 191 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS G 260 GLN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 HIS ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 ASN I 234 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN I 341 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN K 204 GLN K 260 GLN ** K 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS M 142 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 273 ASN O 138 GLN O 260 GLN O 264 ASN ** O 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN Q 245 ASN Q 273 ASN Q 281 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29392 Z= 0.356 Angle : 0.707 6.917 40098 Z= 0.372 Chirality : 0.044 0.152 4574 Planarity : 0.005 0.067 5165 Dihedral : 7.518 66.295 4244 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.70 % Allowed : 30.72 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.45 (0.14), residues: 3679 helix: -1.05 (0.26), residues: 340 sheet: -0.43 (0.14), residues: 1213 loop : -1.27 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 339 HIS 0.019 0.002 HIS I 130 PHE 0.026 0.002 PHE Q 376 TYR 0.027 0.002 TYR I 237 ARG 0.009 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 692 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8184 (p-80) REVERT: C 333 ASN cc_start: 0.8640 (t0) cc_final: 0.8390 (t0) REVERT: E 242 ASP cc_start: 0.4886 (p0) cc_final: 0.4598 (p0) REVERT: E 277 HIS cc_start: 0.3083 (OUTLIER) cc_final: 0.2774 (t70) REVERT: G 6 VAL cc_start: 0.9141 (t) cc_final: 0.8861 (p) REVERT: G 32 GLU cc_start: 0.8261 (tp30) cc_final: 0.7876 (tp30) REVERT: G 75 ASP cc_start: 0.8651 (t0) cc_final: 0.8258 (t0) REVERT: G 117 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7690 (pp20) REVERT: G 202 ASP cc_start: 0.9251 (p0) cc_final: 0.9025 (p0) REVERT: G 216 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8725 (p0) REVERT: G 260 GLN cc_start: 0.8845 (mp-120) cc_final: 0.8340 (mp10) REVERT: G 269 VAL cc_start: 0.8283 (t) cc_final: 0.7879 (m) REVERT: G 310 SER cc_start: 0.9357 (m) cc_final: 0.8920 (p) REVERT: G 351 GLN cc_start: 0.8488 (pp30) cc_final: 0.7973 (pp30) REVERT: G 353 GLN cc_start: 0.7769 (tm130) cc_final: 0.7522 (tm130) REVERT: G 385 ASP cc_start: 0.7492 (t0) cc_final: 0.7106 (t0) REVERT: I 45 THR cc_start: 0.8982 (m) cc_final: 0.8679 (p) REVERT: I 303 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7469 (tm-30) REVERT: I 305 ASN cc_start: 0.8558 (m-40) cc_final: 0.7928 (m-40) REVERT: I 308 GLU cc_start: 0.8513 (pt0) cc_final: 0.8151 (pt0) REVERT: I 338 TYR cc_start: 0.8542 (m-80) cc_final: 0.8245 (m-80) REVERT: I 341 GLN cc_start: 0.8410 (tp40) cc_final: 0.8107 (tt0) REVERT: K 42 LEU cc_start: 0.8741 (mm) cc_final: 0.8436 (mm) REVERT: K 96 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7693 (m) REVERT: K 162 VAL cc_start: 0.8661 (t) cc_final: 0.8371 (m) REVERT: K 217 THR cc_start: 0.8901 (p) cc_final: 0.8606 (p) REVERT: K 351 GLN cc_start: 0.8932 (pt0) cc_final: 0.8689 (pm20) REVERT: K 384 LYS cc_start: 0.5456 (mmtm) cc_final: 0.4788 (mptt) REVERT: M 45 THR cc_start: 0.9178 (m) cc_final: 0.8734 (p) REVERT: M 54 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9144 (pt) REVERT: M 139 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7318 (mt-10) REVERT: M 149 LYS cc_start: 0.9303 (ttmm) cc_final: 0.9061 (ttpp) REVERT: M 303 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8245 (tm-30) REVERT: M 308 GLU cc_start: 0.8706 (pt0) cc_final: 0.8305 (pt0) REVERT: O 123 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8809 (ttp-110) REVERT: O 125 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8421 (p-80) REVERT: O 166 MET cc_start: 0.9682 (mmp) cc_final: 0.9221 (mmm) REVERT: O 216 ASN cc_start: 0.8574 (t0) cc_final: 0.8274 (p0) REVERT: O 310 SER cc_start: 0.9040 (m) cc_final: 0.8450 (t) REVERT: O 376 CYS cc_start: 0.8949 (t) cc_final: 0.8154 (m) REVERT: Q 66 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8354 (mmmt) REVERT: Q 70 MET cc_start: 0.7362 (tpp) cc_final: 0.7153 (tpp) REVERT: Q 281 ASN cc_start: 0.8606 (t160) cc_final: 0.8250 (t0) REVERT: Q 305 ASN cc_start: 0.8762 (m-40) cc_final: 0.8439 (t0) REVERT: Q 393 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8185 (mtt180) outliers start: 149 outliers final: 96 residues processed: 789 average time/residue: 0.7417 time to fit residues: 911.2329 Evaluate side-chains 753 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 651 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 277 HIS Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 369 VAL Chi-restraints excluded: chain M residue 6 PHE Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 281 ASN Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 125 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 273 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 329 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS C 202 ASN C 345 ASN E 66 ASN ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN G 264 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN M 130 HIS M 142 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 ASN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 281 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29392 Z= 0.238 Angle : 0.640 7.164 40098 Z= 0.333 Chirality : 0.044 0.152 4574 Planarity : 0.004 0.057 5165 Dihedral : 7.017 59.832 4234 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.04 % Allowed : 30.27 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.33 (0.14), residues: 3679 helix: -0.76 (0.26), residues: 344 sheet: -0.38 (0.14), residues: 1215 loop : -1.19 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 339 HIS 0.031 0.002 HIS C 130 PHE 0.022 0.002 PHE Q 376 TYR 0.020 0.001 TYR C 237 ARG 0.006 0.000 ARG I 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 672 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6137 (pp20) REVERT: C 308 GLU cc_start: 0.8368 (pt0) cc_final: 0.8063 (pt0) REVERT: C 333 ASN cc_start: 0.8708 (t0) cc_final: 0.8348 (t0) REVERT: G 32 GLU cc_start: 0.8285 (tp30) cc_final: 0.7856 (tp30) REVERT: G 75 ASP cc_start: 0.8766 (t0) cc_final: 0.8310 (t0) REVERT: G 117 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7862 (pp20) REVERT: G 260 GLN cc_start: 0.8872 (mp-120) cc_final: 0.8355 (mp10) REVERT: G 269 VAL cc_start: 0.8177 (t) cc_final: 0.7773 (m) REVERT: G 310 SER cc_start: 0.9306 (m) cc_final: 0.8920 (p) REVERT: G 341 GLU cc_start: 0.8312 (mp0) cc_final: 0.7813 (mp0) REVERT: G 351 GLN cc_start: 0.8386 (pp30) cc_final: 0.7950 (pp30) REVERT: G 353 GLN cc_start: 0.7801 (tm130) cc_final: 0.7533 (tm130) REVERT: I 97 MET cc_start: 0.8456 (tpt) cc_final: 0.7786 (tpp) REVERT: I 237 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5907 (p90) REVERT: I 308 GLU cc_start: 0.8436 (pt0) cc_final: 0.8047 (pt0) REVERT: I 332 ASN cc_start: 0.8781 (m-40) cc_final: 0.8309 (m-40) REVERT: I 338 TYR cc_start: 0.8504 (m-80) cc_final: 0.8123 (m-10) REVERT: K 162 VAL cc_start: 0.8670 (t) cc_final: 0.8399 (m) REVERT: K 199 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8537 (mp10) REVERT: K 217 THR cc_start: 0.8837 (p) cc_final: 0.8582 (p) REVERT: K 260 GLN cc_start: 0.7495 (mp10) cc_final: 0.7285 (mp10) REVERT: K 351 GLN cc_start: 0.8983 (pt0) cc_final: 0.8623 (pm20) REVERT: M 45 THR cc_start: 0.9198 (m) cc_final: 0.8769 (p) REVERT: M 54 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9134 (pt) REVERT: M 70 MET cc_start: 0.6454 (tpp) cc_final: 0.6225 (tpp) REVERT: M 130 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8347 (t-90) REVERT: M 139 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7231 (mt-10) REVERT: M 149 LYS cc_start: 0.9254 (ttmm) cc_final: 0.8981 (ttpp) REVERT: M 303 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8291 (tm-30) REVERT: M 308 GLU cc_start: 0.8563 (pt0) cc_final: 0.8183 (pt0) REVERT: M 366 MET cc_start: 0.6939 (mmm) cc_final: 0.6521 (mpp) REVERT: O 166 MET cc_start: 0.9701 (mmp) cc_final: 0.9239 (mmm) REVERT: O 216 ASN cc_start: 0.8603 (t0) cc_final: 0.8376 (p0) REVERT: O 260 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: O 310 SER cc_start: 0.8999 (m) cc_final: 0.8438 (t) REVERT: O 351 GLN cc_start: 0.8932 (pm20) cc_final: 0.8697 (pm20) REVERT: O 376 CYS cc_start: 0.8758 (t) cc_final: 0.8360 (m) REVERT: O 401 ASP cc_start: 0.7711 (p0) cc_final: 0.7480 (p0) REVERT: Q 45 THR cc_start: 0.9143 (m) cc_final: 0.8689 (p) REVERT: Q 66 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8365 (mmmt) REVERT: Q 303 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8626 (tm-30) REVERT: Q 393 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8227 (mtt180) outliers start: 128 outliers final: 92 residues processed: 748 average time/residue: 0.7856 time to fit residues: 933.5714 Evaluate side-chains 750 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 652 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 400 TYR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 20 ASN Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 386 HIS Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 260 GLN Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 115 PHE Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 349 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN E 191 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 299 ASN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29392 Z= 0.273 Angle : 0.636 9.250 40098 Z= 0.330 Chirality : 0.043 0.144 4574 Planarity : 0.004 0.062 5165 Dihedral : 6.874 59.722 4228 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.57 % Allowed : 28.82 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.35 (0.14), residues: 3679 helix: -0.56 (0.27), residues: 344 sheet: -0.41 (0.14), residues: 1235 loop : -1.25 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 339 HIS 0.017 0.001 HIS M 130 PHE 0.023 0.001 PHE Q 376 TYR 0.024 0.002 TYR C 237 ARG 0.004 0.000 ARG O 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 657 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8273 (p-80) REVERT: A 183 ASP cc_start: 0.6905 (t0) cc_final: 0.6620 (t0) REVERT: A 228 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 306 TYR cc_start: 0.7645 (t80) cc_final: 0.6593 (t80) REVERT: C 308 GLU cc_start: 0.8472 (pt0) cc_final: 0.8159 (pt0) REVERT: C 333 ASN cc_start: 0.8733 (t0) cc_final: 0.8227 (t0) REVERT: C 412 LEU cc_start: 0.8780 (tp) cc_final: 0.8436 (tp) REVERT: G 6 VAL cc_start: 0.9172 (t) cc_final: 0.8869 (p) REVERT: G 32 GLU cc_start: 0.8239 (tp30) cc_final: 0.7632 (tp30) REVERT: G 45 ASP cc_start: 0.8335 (t0) cc_final: 0.8064 (t0) REVERT: G 75 ASP cc_start: 0.8891 (t0) cc_final: 0.8453 (t0) REVERT: G 107 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7752 (p-80) REVERT: G 117 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7895 (pp20) REVERT: G 260 GLN cc_start: 0.8933 (mp-120) cc_final: 0.8482 (mp10) REVERT: G 269 VAL cc_start: 0.8281 (t) cc_final: 0.8016 (m) REVERT: G 270 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.7874 (m110) REVERT: G 310 SER cc_start: 0.9121 (m) cc_final: 0.8881 (p) REVERT: G 341 GLU cc_start: 0.8294 (mp0) cc_final: 0.7803 (mp0) REVERT: G 351 GLN cc_start: 0.8491 (pp30) cc_final: 0.8032 (pp30) REVERT: G 353 GLN cc_start: 0.7927 (tm130) cc_final: 0.7653 (tm130) REVERT: I 303 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7620 (tm-30) REVERT: I 305 ASN cc_start: 0.8716 (t0) cc_final: 0.8254 (t0) REVERT: I 332 ASN cc_start: 0.8725 (m-40) cc_final: 0.8469 (m-40) REVERT: I 338 TYR cc_start: 0.8555 (m-80) cc_final: 0.8221 (m-80) REVERT: K 162 VAL cc_start: 0.8696 (t) cc_final: 0.8390 (m) REVERT: K 173 PHE cc_start: 0.9207 (m-80) cc_final: 0.8962 (m-80) REVERT: K 199 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8659 (mp10) REVERT: K 217 THR cc_start: 0.8976 (p) cc_final: 0.8721 (p) REVERT: K 260 GLN cc_start: 0.7540 (mp10) cc_final: 0.7273 (mp10) REVERT: K 351 GLN cc_start: 0.9136 (pt0) cc_final: 0.8858 (pm20) REVERT: K 384 LYS cc_start: 0.4866 (mmtt) cc_final: 0.4655 (mmtt) REVERT: M 45 THR cc_start: 0.9247 (m) cc_final: 0.8782 (p) REVERT: M 70 MET cc_start: 0.6362 (tpp) cc_final: 0.6115 (tpp) REVERT: M 115 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8673 (p90) REVERT: M 139 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7443 (mt-10) REVERT: M 149 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8937 (ttpp) REVERT: M 303 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8313 (tm-30) REVERT: M 306 TYR cc_start: 0.7991 (t80) cc_final: 0.7300 (t80) REVERT: M 308 GLU cc_start: 0.8510 (pt0) cc_final: 0.7938 (pt0) REVERT: O 125 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8392 (p-80) REVERT: O 166 MET cc_start: 0.9704 (mmp) cc_final: 0.9225 (mmm) REVERT: O 216 ASN cc_start: 0.8555 (t0) cc_final: 0.8294 (p0) REVERT: O 260 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: O 310 SER cc_start: 0.9024 (m) cc_final: 0.8757 (p) REVERT: O 351 GLN cc_start: 0.8999 (pm20) cc_final: 0.8735 (pm20) REVERT: O 401 ASP cc_start: 0.7918 (p0) cc_final: 0.7647 (p0) REVERT: Q 66 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8405 (mmmt) REVERT: Q 236 GLN cc_start: 0.6728 (tm-30) cc_final: 0.6387 (tm-30) REVERT: Q 393 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8272 (mtt180) outliers start: 145 outliers final: 118 residues processed: 752 average time/residue: 0.7209 time to fit residues: 851.2610 Evaluate side-chains 758 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 632 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 386 HIS Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 313 HIS Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 125 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 260 GLN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS ** M 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29392 Z= 0.373 Angle : 0.683 9.243 40098 Z= 0.361 Chirality : 0.044 0.163 4574 Planarity : 0.005 0.063 5165 Dihedral : 6.997 59.351 4228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.05 % Favored : 90.87 % Rotamer: Outliers : 5.83 % Allowed : 27.85 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.64 (0.14), residues: 3679 helix: -0.45 (0.27), residues: 344 sheet: -0.65 (0.14), residues: 1283 loop : -1.50 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 339 HIS 0.011 0.002 HIS G 230 PHE 0.019 0.002 PHE Q 376 TYR 0.028 0.002 TYR I 237 ARG 0.010 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 635 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8103 (p-80) REVERT: A 228 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8720 (p) REVERT: C 333 ASN cc_start: 0.8792 (t0) cc_final: 0.8213 (t0) REVERT: C 412 LEU cc_start: 0.8884 (tp) cc_final: 0.8621 (tp) REVERT: G 6 VAL cc_start: 0.9334 (t) cc_final: 0.9070 (p) REVERT: G 9 ASN cc_start: 0.9209 (t0) cc_final: 0.8988 (t0) REVERT: G 75 ASP cc_start: 0.9014 (t0) cc_final: 0.8560 (t0) REVERT: G 117 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: G 310 SER cc_start: 0.9177 (m) cc_final: 0.8885 (p) REVERT: G 341 GLU cc_start: 0.8381 (mp0) cc_final: 0.7864 (mp0) REVERT: G 351 GLN cc_start: 0.8636 (pp30) cc_final: 0.8067 (pp30) REVERT: I 332 ASN cc_start: 0.8744 (m-40) cc_final: 0.8465 (m-40) REVERT: I 333 ASN cc_start: 0.8492 (t0) cc_final: 0.8285 (t0) REVERT: I 338 TYR cc_start: 0.8580 (m-80) cc_final: 0.8152 (m-80) REVERT: K 17 THR cc_start: 0.9153 (m) cc_final: 0.8715 (p) REVERT: K 187 MET cc_start: 0.7798 (tmm) cc_final: 0.7222 (tmm) REVERT: K 217 THR cc_start: 0.9072 (p) cc_final: 0.8824 (p) REVERT: K 260 GLN cc_start: 0.7986 (mp10) cc_final: 0.7644 (mp10) REVERT: M 45 THR cc_start: 0.9285 (m) cc_final: 0.8848 (p) REVERT: M 70 MET cc_start: 0.6545 (tpp) cc_final: 0.6326 (tpp) REVERT: M 115 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8827 (p90) REVERT: M 149 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8956 (ttpp) REVERT: M 201 CYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8756 (t) REVERT: M 303 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8378 (tm-30) REVERT: M 315 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8587 (mmtm) REVERT: O 125 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8139 (p90) REVERT: O 166 MET cc_start: 0.9688 (mmp) cc_final: 0.9174 (mmm) REVERT: O 199 GLN cc_start: 0.7833 (mp10) cc_final: 0.7499 (mp10) REVERT: O 260 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: O 310 SER cc_start: 0.9069 (m) cc_final: 0.8789 (p) REVERT: O 351 GLN cc_start: 0.9075 (pm20) cc_final: 0.8743 (pm20) REVERT: O 376 CYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8685 (m) REVERT: Q 32 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8890 (mp) REVERT: Q 143 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7592 (p) REVERT: Q 306 TYR cc_start: 0.8377 (t80) cc_final: 0.7693 (t80) REVERT: Q 308 GLU cc_start: 0.8682 (pt0) cc_final: 0.8176 (pt0) outliers start: 185 outliers final: 142 residues processed: 756 average time/residue: 0.7412 time to fit residues: 891.2055 Evaluate side-chains 775 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 623 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 400 TYR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 259 CYS Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 6 PHE Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 281 ASN Chi-restraints excluded: chain M residue 313 HIS Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 394 ARG Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 125 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 155 THR Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 260 GLN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 376 CYS Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 232 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 0.3980 chunk 315 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 350 optimal weight: 0.0010 chunk 290 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 HIS ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 400 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29392 Z= 0.211 Angle : 0.632 7.533 40098 Z= 0.325 Chirality : 0.045 0.200 4574 Planarity : 0.004 0.059 5165 Dihedral : 6.599 59.552 4219 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.07 % Allowed : 29.58 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.39 (0.14), residues: 3679 helix: -0.27 (0.28), residues: 344 sheet: -0.50 (0.15), residues: 1235 loop : -1.29 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 339 HIS 0.009 0.001 HIS G 230 PHE 0.020 0.002 PHE Q 141 TYR 0.026 0.001 TYR C 237 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 651 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8291 (p-80) REVERT: A 183 ASP cc_start: 0.7037 (t0) cc_final: 0.6747 (t0) REVERT: C 305 ASN cc_start: 0.8790 (m-40) cc_final: 0.8487 (m-40) REVERT: C 333 ASN cc_start: 0.8799 (t0) cc_final: 0.8165 (t0) REVERT: C 366 MET cc_start: 0.7816 (mmm) cc_final: 0.6995 (tmm) REVERT: C 412 LEU cc_start: 0.8860 (tp) cc_final: 0.8516 (tp) REVERT: G 6 VAL cc_start: 0.9242 (t) cc_final: 0.8952 (p) REVERT: G 9 ASN cc_start: 0.9184 (t0) cc_final: 0.8933 (t0) REVERT: G 75 ASP cc_start: 0.8974 (t0) cc_final: 0.8495 (t0) REVERT: G 117 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: G 310 SER cc_start: 0.9128 (m) cc_final: 0.8840 (p) REVERT: G 351 GLN cc_start: 0.8628 (pp30) cc_final: 0.8174 (pp30) REVERT: I 57 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8703 (ttpt) REVERT: I 333 ASN cc_start: 0.8475 (t0) cc_final: 0.8253 (t0) REVERT: I 338 TYR cc_start: 0.8485 (m-80) cc_final: 0.8156 (m-80) REVERT: K 17 THR cc_start: 0.9125 (m) cc_final: 0.8689 (p) REVERT: K 187 MET cc_start: 0.7815 (tmm) cc_final: 0.7179 (tmm) REVERT: K 199 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8702 (mm-40) REVERT: K 217 THR cc_start: 0.9028 (p) cc_final: 0.8773 (p) REVERT: K 384 LYS cc_start: 0.5192 (mmtt) cc_final: 0.4970 (mmtt) REVERT: K 385 ASP cc_start: 0.7118 (t0) cc_final: 0.6877 (t0) REVERT: M 45 THR cc_start: 0.9273 (m) cc_final: 0.8823 (p) REVERT: M 70 MET cc_start: 0.6503 (tpp) cc_final: 0.6286 (tpp) REVERT: M 115 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8561 (p90) REVERT: M 149 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8902 (ttpp) REVERT: M 201 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8725 (t) REVERT: M 300 MET cc_start: 0.8407 (mmm) cc_final: 0.8014 (mtp) REVERT: M 315 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8556 (mmtm) REVERT: O 166 MET cc_start: 0.9724 (mmp) cc_final: 0.9210 (mmm) REVERT: O 199 GLN cc_start: 0.7663 (mp10) cc_final: 0.7323 (mp10) REVERT: O 281 ASP cc_start: 0.9161 (t0) cc_final: 0.8953 (m-30) REVERT: O 310 SER cc_start: 0.8970 (m) cc_final: 0.8704 (p) REVERT: O 351 GLN cc_start: 0.9092 (pm20) cc_final: 0.8748 (pm20) REVERT: O 376 CYS cc_start: 0.8955 (t) cc_final: 0.8369 (m) REVERT: Q 66 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8435 (mmmt) REVERT: Q 366 MET cc_start: 0.6531 (mmm) cc_final: 0.6234 (ttp) REVERT: Q 393 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8388 (mtt180) outliers start: 129 outliers final: 108 residues processed: 736 average time/residue: 0.7305 time to fit residues: 844.4384 Evaluate side-chains 734 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 622 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 400 TYR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 20 ASN Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 200 LYS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 379 LEU Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29392 Z= 0.237 Angle : 0.636 8.044 40098 Z= 0.326 Chirality : 0.044 0.176 4574 Planarity : 0.004 0.057 5165 Dihedral : 6.543 58.126 4219 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.38 % Allowed : 29.58 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.37 (0.14), residues: 3679 helix: -0.23 (0.28), residues: 344 sheet: -0.49 (0.15), residues: 1235 loop : -1.28 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 194 HIS 0.031 0.001 HIS I 232 PHE 0.022 0.002 PHE I 259 TYR 0.026 0.001 TYR C 237 ARG 0.006 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 626 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8230 (p-80) REVERT: A 183 ASP cc_start: 0.7041 (t0) cc_final: 0.6794 (t0) REVERT: C 305 ASN cc_start: 0.8817 (m-40) cc_final: 0.8508 (m-40) REVERT: C 333 ASN cc_start: 0.8828 (t0) cc_final: 0.8174 (t0) REVERT: C 366 MET cc_start: 0.7766 (mmm) cc_final: 0.6934 (tmm) REVERT: C 412 LEU cc_start: 0.8899 (tp) cc_final: 0.8590 (tp) REVERT: G 6 VAL cc_start: 0.9287 (t) cc_final: 0.9018 (p) REVERT: G 117 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: G 310 SER cc_start: 0.9150 (m) cc_final: 0.8866 (p) REVERT: G 341 GLU cc_start: 0.8613 (mp0) cc_final: 0.8124 (mp0) REVERT: G 351 GLN cc_start: 0.8717 (pp30) cc_final: 0.8298 (pp30) REVERT: I 47 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7998 (mtmm) REVERT: I 57 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8729 (ttpt) REVERT: I 333 ASN cc_start: 0.8507 (t0) cc_final: 0.8292 (t0) REVERT: I 338 TYR cc_start: 0.8539 (m-80) cc_final: 0.8129 (m-80) REVERT: K 17 THR cc_start: 0.9039 (m) cc_final: 0.8624 (p) REVERT: K 27 MET cc_start: 0.6958 (tpp) cc_final: 0.6273 (mtm) REVERT: K 173 PHE cc_start: 0.9268 (m-80) cc_final: 0.9011 (m-80) REVERT: K 187 MET cc_start: 0.7832 (tmm) cc_final: 0.7225 (tmm) REVERT: K 199 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8784 (mm-40) REVERT: K 217 THR cc_start: 0.9080 (p) cc_final: 0.8828 (p) REVERT: M 45 THR cc_start: 0.9267 (m) cc_final: 0.8818 (p) REVERT: M 115 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8498 (p90) REVERT: M 149 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8985 (ttpp) REVERT: M 201 CYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8645 (t) REVERT: M 300 MET cc_start: 0.8411 (mmm) cc_final: 0.8123 (mtp) REVERT: M 303 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8203 (tm-30) REVERT: O 107 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8109 (p-80) REVERT: O 166 MET cc_start: 0.9713 (mmp) cc_final: 0.9227 (mmm) REVERT: O 310 SER cc_start: 0.8990 (m) cc_final: 0.8623 (p) REVERT: O 351 GLN cc_start: 0.9123 (pm20) cc_final: 0.8789 (pm20) REVERT: O 376 CYS cc_start: 0.8979 (t) cc_final: 0.8393 (m) REVERT: Q 66 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8414 (mmmt) REVERT: Q 236 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6521 (tm-30) REVERT: Q 366 MET cc_start: 0.6608 (mmm) cc_final: 0.6251 (ttp) REVERT: Q 393 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8420 (mtt180) outliers start: 139 outliers final: 122 residues processed: 716 average time/residue: 0.7353 time to fit residues: 835.0447 Evaluate side-chains 746 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 618 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 6 PHE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 107 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 379 LEU Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN C 273 ASN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 GLN ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29392 Z= 0.238 Angle : 0.631 8.396 40098 Z= 0.323 Chirality : 0.044 0.182 4574 Planarity : 0.004 0.072 5165 Dihedral : 6.492 57.091 4218 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.64 % Allowed : 29.27 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.38 (0.14), residues: 3679 helix: -0.11 (0.29), residues: 336 sheet: -0.52 (0.15), residues: 1235 loop : -1.29 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 194 HIS 0.009 0.001 HIS I 232 PHE 0.028 0.002 PHE I 259 TYR 0.026 0.001 TYR C 237 ARG 0.010 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 628 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8229 (p0) cc_final: 0.7652 (p0) REVERT: A 125 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8281 (p-80) REVERT: C 69 TYR cc_start: 0.6783 (p90) cc_final: 0.6474 (p90) REVERT: C 305 ASN cc_start: 0.8820 (m-40) cc_final: 0.8495 (m-40) REVERT: C 333 ASN cc_start: 0.8832 (t0) cc_final: 0.8139 (t0) REVERT: C 358 TYR cc_start: 0.8414 (m-80) cc_final: 0.8212 (m-80) REVERT: C 366 MET cc_start: 0.7719 (mmm) cc_final: 0.6972 (tmm) REVERT: C 412 LEU cc_start: 0.8930 (tp) cc_final: 0.8629 (tp) REVERT: G 6 VAL cc_start: 0.9303 (t) cc_final: 0.9035 (p) REVERT: G 32 GLU cc_start: 0.8223 (tp30) cc_final: 0.7900 (tp30) REVERT: G 45 ASP cc_start: 0.8490 (t0) cc_final: 0.8128 (t0) REVERT: G 75 ASP cc_start: 0.9063 (t0) cc_final: 0.8583 (t0) REVERT: G 87 PHE cc_start: 0.9038 (m-80) cc_final: 0.8693 (m-80) REVERT: G 107 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7571 (p-80) REVERT: G 117 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: G 251 LEU cc_start: 0.9289 (mt) cc_final: 0.9058 (mt) REVERT: G 310 SER cc_start: 0.9151 (m) cc_final: 0.8867 (p) REVERT: G 341 GLU cc_start: 0.8579 (mp0) cc_final: 0.8079 (mp0) REVERT: G 351 GLN cc_start: 0.8773 (pp30) cc_final: 0.8347 (pp30) REVERT: G 355 SER cc_start: 0.7436 (p) cc_final: 0.6772 (p) REVERT: I 47 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8044 (mtmm) REVERT: I 57 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8727 (ttpt) REVERT: I 303 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8211 (tm-30) REVERT: I 333 ASN cc_start: 0.8533 (t0) cc_final: 0.8297 (t0) REVERT: I 338 TYR cc_start: 0.8516 (m-80) cc_final: 0.8108 (m-80) REVERT: K 17 THR cc_start: 0.9042 (m) cc_final: 0.8632 (p) REVERT: K 173 PHE cc_start: 0.9282 (m-80) cc_final: 0.9040 (m-80) REVERT: K 187 MET cc_start: 0.7866 (tmm) cc_final: 0.7291 (tmm) REVERT: K 199 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8778 (mm-40) REVERT: K 217 THR cc_start: 0.9126 (p) cc_final: 0.8875 (p) REVERT: M 45 THR cc_start: 0.9273 (m) cc_final: 0.8826 (p) REVERT: M 115 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8496 (p90) REVERT: M 149 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8995 (ttpp) REVERT: M 201 CYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8686 (t) REVERT: M 300 MET cc_start: 0.8378 (mmm) cc_final: 0.8117 (mtp) REVERT: M 303 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8224 (tm-30) REVERT: M 315 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8556 (mmtm) REVERT: O 166 MET cc_start: 0.9718 (mmp) cc_final: 0.9240 (mmm) REVERT: O 199 GLN cc_start: 0.7656 (mp10) cc_final: 0.7314 (mp10) REVERT: O 310 SER cc_start: 0.9007 (m) cc_final: 0.8633 (p) REVERT: O 351 GLN cc_start: 0.9154 (pm20) cc_final: 0.8810 (pm20) REVERT: O 376 CYS cc_start: 0.8976 (t) cc_final: 0.8414 (m) REVERT: Q 66 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8391 (mmmt) REVERT: Q 236 GLN cc_start: 0.6770 (tm-30) cc_final: 0.6558 (tm-30) REVERT: Q 321 VAL cc_start: 0.9546 (m) cc_final: 0.9210 (p) REVERT: Q 366 MET cc_start: 0.6677 (mmm) cc_final: 0.6295 (ttp) REVERT: Q 393 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8416 (mtt180) outliers start: 147 outliers final: 130 residues processed: 725 average time/residue: 0.7376 time to fit residues: 850.2049 Evaluate side-chains 750 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 614 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 331 HIS Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 347 GLU Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 6 PHE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 232 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 379 LEU Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 195 optimal weight: 0.0010 chunk 141 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29392 Z= 0.214 Angle : 0.630 8.314 40098 Z= 0.321 Chirality : 0.044 0.176 4574 Planarity : 0.004 0.055 5165 Dihedral : 6.390 56.346 4218 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.32 % Allowed : 29.55 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.29 (0.14), residues: 3679 helix: -0.05 (0.29), residues: 332 sheet: -0.44 (0.15), residues: 1230 loop : -1.24 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 89 HIS 0.007 0.001 HIS C 170 PHE 0.024 0.001 PHE I 259 TYR 0.025 0.001 TYR C 237 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 630 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8261 (p-80) REVERT: A 183 ASP cc_start: 0.7055 (t0) cc_final: 0.6737 (t0) REVERT: C 305 ASN cc_start: 0.8827 (m-40) cc_final: 0.8493 (m-40) REVERT: C 327 GLU cc_start: 0.9144 (pt0) cc_final: 0.8789 (pt0) REVERT: C 333 ASN cc_start: 0.8877 (t0) cc_final: 0.8254 (t0) REVERT: C 358 TYR cc_start: 0.8420 (m-80) cc_final: 0.8202 (m-80) REVERT: C 366 MET cc_start: 0.7657 (mmm) cc_final: 0.6884 (tmm) REVERT: C 412 LEU cc_start: 0.9018 (tp) cc_final: 0.8749 (tp) REVERT: G 6 VAL cc_start: 0.9282 (t) cc_final: 0.9020 (p) REVERT: G 32 GLU cc_start: 0.8156 (tp30) cc_final: 0.7813 (tp30) REVERT: G 45 ASP cc_start: 0.8492 (t0) cc_final: 0.8133 (t0) REVERT: G 75 ASP cc_start: 0.9097 (t0) cc_final: 0.8601 (t0) REVERT: G 87 PHE cc_start: 0.9014 (m-80) cc_final: 0.8709 (m-80) REVERT: G 107 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7561 (p-80) REVERT: G 117 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: G 251 LEU cc_start: 0.9267 (mt) cc_final: 0.9005 (mt) REVERT: G 310 SER cc_start: 0.9130 (m) cc_final: 0.8871 (p) REVERT: G 341 GLU cc_start: 0.8470 (mp0) cc_final: 0.8091 (mp0) REVERT: G 351 GLN cc_start: 0.8783 (pp30) cc_final: 0.8350 (pp30) REVERT: G 417 VAL cc_start: 0.8384 (m) cc_final: 0.8093 (p) REVERT: I 47 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8043 (mtmm) REVERT: I 303 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8213 (tm-30) REVERT: I 333 ASN cc_start: 0.8536 (t0) cc_final: 0.8314 (t0) REVERT: I 338 TYR cc_start: 0.8544 (m-80) cc_final: 0.8112 (m-80) REVERT: K 17 THR cc_start: 0.9048 (m) cc_final: 0.8616 (p) REVERT: K 27 MET cc_start: 0.7144 (tpp) cc_final: 0.6686 (mtp) REVERT: K 173 PHE cc_start: 0.9297 (m-80) cc_final: 0.9053 (m-80) REVERT: K 187 MET cc_start: 0.7897 (tmm) cc_final: 0.7325 (tmm) REVERT: K 199 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8691 (mp10) REVERT: K 217 THR cc_start: 0.9114 (p) cc_final: 0.8852 (p) REVERT: K 385 ASP cc_start: 0.6983 (t0) cc_final: 0.6740 (t0) REVERT: M 26 HIS cc_start: 0.8440 (m90) cc_final: 0.7898 (m90) REVERT: M 45 THR cc_start: 0.9272 (m) cc_final: 0.8832 (p) REVERT: M 149 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8982 (ttpp) REVERT: M 201 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8680 (t) REVERT: M 300 MET cc_start: 0.8331 (mmm) cc_final: 0.8100 (mtp) REVERT: M 303 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8228 (tm-30) REVERT: M 308 GLU cc_start: 0.8432 (pt0) cc_final: 0.7954 (pt0) REVERT: M 361 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7295 (mt-10) REVERT: O 166 MET cc_start: 0.9722 (mmp) cc_final: 0.9253 (mmm) REVERT: O 310 SER cc_start: 0.8993 (m) cc_final: 0.8607 (p) REVERT: O 351 GLN cc_start: 0.9156 (pm20) cc_final: 0.8805 (pm20) REVERT: O 376 CYS cc_start: 0.8952 (t) cc_final: 0.8400 (m) REVERT: Q 66 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8347 (mmmt) REVERT: Q 70 MET cc_start: 0.7672 (tpp) cc_final: 0.7277 (tpp) REVERT: Q 236 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6572 (tm-30) REVERT: Q 321 VAL cc_start: 0.9543 (m) cc_final: 0.9209 (p) REVERT: Q 366 MET cc_start: 0.6628 (mmm) cc_final: 0.6269 (ttp) outliers start: 137 outliers final: 124 residues processed: 721 average time/residue: 0.7341 time to fit residues: 837.8096 Evaluate side-chains 743 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 614 time to evaluate : 3.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 278 HIS Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 200 LYS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 107 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 379 LEU Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 403 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 0.6980 chunk 343 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 163 optimal weight: 0.3980 chunk 239 optimal weight: 4.9990 chunk 360 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29392 Z= 0.196 Angle : 0.636 8.901 40098 Z= 0.323 Chirality : 0.045 0.177 4574 Planarity : 0.004 0.058 5165 Dihedral : 6.324 55.945 4218 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.72 % Allowed : 30.12 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.26 (0.14), residues: 3679 helix: -0.05 (0.29), residues: 332 sheet: -0.44 (0.15), residues: 1247 loop : -1.20 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 194 HIS 0.007 0.001 HIS M 170 PHE 0.016 0.001 PHE Q 376 TYR 0.025 0.001 TYR C 237 ARG 0.006 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 642 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8305 (p-80) REVERT: A 183 ASP cc_start: 0.6992 (t0) cc_final: 0.6664 (t0) REVERT: C 300 MET cc_start: 0.8596 (tpt) cc_final: 0.8276 (tpt) REVERT: C 305 ASN cc_start: 0.8815 (m-40) cc_final: 0.8477 (m-40) REVERT: C 327 GLU cc_start: 0.9143 (pt0) cc_final: 0.8816 (pt0) REVERT: C 333 ASN cc_start: 0.8873 (t0) cc_final: 0.8243 (t0) REVERT: C 358 TYR cc_start: 0.8466 (m-80) cc_final: 0.8237 (m-80) REVERT: C 366 MET cc_start: 0.7618 (mmm) cc_final: 0.6770 (tmm) REVERT: C 412 LEU cc_start: 0.9007 (tp) cc_final: 0.8742 (tp) REVERT: G 6 VAL cc_start: 0.9222 (t) cc_final: 0.8960 (p) REVERT: G 32 GLU cc_start: 0.8148 (tp30) cc_final: 0.7689 (tp30) REVERT: G 45 ASP cc_start: 0.8483 (t0) cc_final: 0.8131 (t0) REVERT: G 75 ASP cc_start: 0.9111 (t0) cc_final: 0.8601 (t0) REVERT: G 87 PHE cc_start: 0.8988 (m-80) cc_final: 0.8685 (m-80) REVERT: G 107 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7536 (p-80) REVERT: G 117 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8018 (pm20) REVERT: G 251 LEU cc_start: 0.9275 (mt) cc_final: 0.8999 (mt) REVERT: G 310 SER cc_start: 0.9116 (m) cc_final: 0.8867 (p) REVERT: G 341 GLU cc_start: 0.8495 (mp0) cc_final: 0.8041 (mp0) REVERT: G 351 GLN cc_start: 0.8802 (pp30) cc_final: 0.8357 (pp30) REVERT: G 385 ASP cc_start: 0.8211 (m-30) cc_final: 0.7503 (t0) REVERT: G 417 VAL cc_start: 0.8383 (m) cc_final: 0.8094 (p) REVERT: I 47 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: I 303 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8212 (tm-30) REVERT: I 338 TYR cc_start: 0.8540 (m-80) cc_final: 0.8121 (m-80) REVERT: K 17 THR cc_start: 0.9022 (m) cc_final: 0.8590 (p) REVERT: K 27 MET cc_start: 0.7162 (tpp) cc_final: 0.6503 (mtt) REVERT: K 173 PHE cc_start: 0.9292 (m-80) cc_final: 0.9060 (m-80) REVERT: K 187 MET cc_start: 0.7900 (tmm) cc_final: 0.7324 (tmm) REVERT: K 217 THR cc_start: 0.9110 (p) cc_final: 0.8396 (p) REVERT: K 331 HIS cc_start: 0.8392 (t70) cc_final: 0.8100 (t70) REVERT: K 385 ASP cc_start: 0.6912 (t0) cc_final: 0.6659 (t0) REVERT: M 26 HIS cc_start: 0.8449 (m90) cc_final: 0.7896 (m90) REVERT: M 45 THR cc_start: 0.9263 (m) cc_final: 0.8832 (p) REVERT: M 201 CYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8665 (t) REVERT: M 300 MET cc_start: 0.8323 (mmm) cc_final: 0.8114 (mtp) REVERT: M 303 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8170 (tm-30) REVERT: M 361 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7218 (mt-10) REVERT: O 166 MET cc_start: 0.9723 (mmp) cc_final: 0.9264 (mmm) REVERT: O 310 SER cc_start: 0.8961 (m) cc_final: 0.8287 (t) REVERT: O 351 GLN cc_start: 0.9125 (pm20) cc_final: 0.8806 (pm20) REVERT: O 376 CYS cc_start: 0.8933 (t) cc_final: 0.8387 (m) REVERT: Q 66 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8311 (mmmt) REVERT: Q 70 MET cc_start: 0.7611 (tpp) cc_final: 0.7270 (tpp) REVERT: Q 321 VAL cc_start: 0.9544 (m) cc_final: 0.9212 (p) REVERT: Q 341 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7010 (pt0) REVERT: Q 366 MET cc_start: 0.6583 (mmm) cc_final: 0.6238 (ttp) REVERT: Q 393 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8747 (mmm-85) outliers start: 118 outliers final: 110 residues processed: 721 average time/residue: 0.7589 time to fit residues: 871.5941 Evaluate side-chains 745 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 630 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 237 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 387 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 115 PHE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 200 LYS Chi-restraints excluded: chain M residue 201 CYS Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 239 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 376 PHE Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 107 HIS Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain O residue 250 SER Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 387 ILE Chi-restraints excluded: chain O residue 421 VAL Chi-restraints excluded: chain Q residue 6 PHE Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 127 HIS Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 237 TYR Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 296 SER Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 341 GLN Chi-restraints excluded: chain Q residue 376 PHE Chi-restraints excluded: chain Q residue 379 LEU Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 403 THR Chi-restraints excluded: chain Q residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 264 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 287 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 295 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 HIS O 204 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 260 GLN ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.076502 restraints weight = 253090.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.080318 restraints weight = 94784.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082591 restraints weight = 48540.238| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29392 Z= 0.275 Angle : 0.650 8.807 40098 Z= 0.335 Chirality : 0.044 0.180 4574 Planarity : 0.004 0.080 5165 Dihedral : 6.439 57.816 4218 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.94 % Allowed : 30.15 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.36 (0.14), residues: 3679 helix: -0.05 (0.29), residues: 336 sheet: -0.46 (0.14), residues: 1278 loop : -1.33 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 89 HIS 0.006 0.001 HIS G 253 PHE 0.016 0.002 PHE A 95 TYR 0.029 0.002 TYR C 237 ARG 0.010 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13307.48 seconds wall clock time: 230 minutes 56.87 seconds (13856.87 seconds total)