Starting phenix.real_space_refine on Wed Feb 14 03:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evm_31329/02_2024/7evm_31329_trim_updated.pdb" } resolution = 2.5 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= -0.001 sd= 0.023 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 48 5.16 5 Cl 2 4.86 5 C 5445 2.51 5 N 1445 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 348": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Residue "R GLU 423": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8462 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1957 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2515 Unusual residues: {'CLR': 6, 'HNO': 1} Classifications: {'peptide': 282, 'undetermined': 7} Link IDs: {'PTRANS': 5, 'TRANS': 276, None: 7} Not linked: pdbres="HIS R 424 " pdbres="HNO R 501 " Not linked: pdbres="HNO R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="CLR R 504 " Not linked: pdbres="CLR R 504 " pdbres="CLR R 505 " ... (remaining 2 not shown) Chain breaks: 2 Time building chain proxies: 4.82, per 1000 atoms: 0.57 Number of scatterers: 8462 At special positions: 0 Unit cell: (82.555, 95.095, 131.67, 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) Cl 2 17.00 S 48 16.00 O 1522 8.00 N 1445 7.00 C 5445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.06 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.736A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.638A pdb=" N TRP A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.628A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.938A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.572A pdb=" N ARG A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 388 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.301A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 137 through 143 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 175 through 210 Processing helix chain 'R' and resid 218 through 223 Processing helix chain 'R' and resid 227 through 256 Processing helix chain 'R' and resid 264 through 291 Proline residue: R 277 - end of helix removed outlier: 3.544A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.046A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 346 through 360 removed outlier: 3.714A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 367 No H-bonds generated for 'chain 'R' and resid 364 through 367' Processing helix chain 'R' and resid 377 through 403 removed outlier: 3.553A pdb=" N THR R 386 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 423 removed outlier: 3.867A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.481A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.703A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.516A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.761A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.601A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.460A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.598A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.762A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.021A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1083 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: 2.40 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1938 1.33 - 1.45: 2088 1.45 - 1.58: 4557 1.58 - 1.71: 5 1.71 - 1.83: 68 Bond restraints: 8656 Sorted by residual: bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.32e-02 5.74e+03 1.59e+01 bond pdb=" C13 CLR R 506 " pdb=" C18 CLR R 506 " ideal model delta sigma weight residual 1.532 1.597 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C LEU R 311 " pdb=" O LEU R 311 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" C13 CLR R 507 " pdb=" C18 CLR R 507 " ideal model delta sigma weight residual 1.532 1.597 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" N LYS R 197 " pdb=" CA LYS R 197 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.20e-02 6.94e+03 1.04e+01 ... (remaining 8651 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.63: 123 105.63 - 112.79: 4671 112.79 - 119.96: 3070 119.96 - 127.12: 3801 127.12 - 134.29: 93 Bond angle restraints: 11758 Sorted by residual: angle pdb=" N PHE R 143 " pdb=" CA PHE R 143 " pdb=" C PHE R 143 " ideal model delta sigma weight residual 112.92 99.77 13.15 1.23e+00 6.61e-01 1.14e+02 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 110.42 103.67 6.75 9.60e-01 1.09e+00 4.94e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 114.03 122.66 -8.63 1.23e+00 6.61e-01 4.93e+01 angle pdb=" N GLU R 292 " pdb=" CA GLU R 292 " pdb=" C GLU R 292 " ideal model delta sigma weight residual 110.17 120.09 -9.92 1.51e+00 4.39e-01 4.31e+01 angle pdb=" C12 HNO R 501 " pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 101.46 118.59 -17.13 3.00e+00 1.11e-01 3.26e+01 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 4743 17.00 - 34.01: 495 34.01 - 51.01: 123 51.01 - 68.01: 34 68.01 - 85.02: 8 Dihedral angle restraints: 5403 sinusoidal: 2381 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 160.72 -67.72 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -132.03 9.43 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1158 0.079 - 0.159: 142 0.159 - 0.238: 14 0.238 - 0.318: 5 0.318 - 0.397: 6 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLU R 292 " pdb=" N GLU R 292 " pdb=" C GLU R 292 " pdb=" CB GLU R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 1322 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 410 " 0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C GLN R 410 " -0.090 2.00e-02 2.50e+03 pdb=" O GLN R 410 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU R 411 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 198 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ASP R 198 " -0.078 2.00e-02 2.50e+03 pdb=" O ASP R 198 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA R 199 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.020 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG N 98 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.030 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.025 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 443 2.72 - 3.26: 8785 3.26 - 3.81: 14391 3.81 - 4.35: 18429 4.35 - 4.90: 30264 Nonbonded interactions: 72312 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.175 2.440 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.222 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.265 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.282 2.440 ... (remaining 72307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8656 Z= 0.333 Angle : 0.888 17.132 11758 Z= 0.506 Chirality : 0.061 0.397 1325 Planarity : 0.005 0.052 1454 Dihedral : 15.265 85.018 3440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.36 % Allowed : 7.51 % Favored : 89.13 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1019 helix: -1.35 (0.23), residues: 384 sheet: -1.43 (0.31), residues: 209 loop : -1.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 PHE 0.017 0.002 PHE R 280 TYR 0.028 0.002 TYR R 148 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 282 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8536 (tt0) cc_final: 0.8030 (tt0) REVERT: A 215 ASP cc_start: 0.7802 (t0) cc_final: 0.7307 (t0) REVERT: A 325 THR cc_start: 0.8755 (m) cc_final: 0.8499 (p) REVERT: A 339 TYR cc_start: 0.7798 (m-80) cc_final: 0.7525 (m-80) REVERT: A 343 ASP cc_start: 0.8072 (m-30) cc_final: 0.7510 (m-30) REVERT: A 370 GLU cc_start: 0.7996 (pm20) cc_final: 0.7631 (pm20) REVERT: A 378 ASP cc_start: 0.7259 (m-30) cc_final: 0.6767 (m-30) REVERT: A 381 ASP cc_start: 0.8350 (t0) cc_final: 0.8112 (t0) REVERT: B 44 GLN cc_start: 0.7955 (pt0) cc_final: 0.7693 (pt0) REVERT: B 47 THR cc_start: 0.8847 (t) cc_final: 0.8562 (m) REVERT: B 124 TYR cc_start: 0.8361 (m-80) cc_final: 0.7914 (m-80) REVERT: B 132 ASN cc_start: 0.6821 (p0) cc_final: 0.6370 (p0) REVERT: B 138 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 175 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7223 (pp30) REVERT: B 217 MET cc_start: 0.7127 (ptt) cc_final: 0.6894 (ptt) REVERT: B 226 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 228 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 230 ASN cc_start: 0.8282 (m-40) cc_final: 0.8033 (m-40) REVERT: B 243 THR cc_start: 0.7847 (p) cc_final: 0.7568 (p) REVERT: B 291 ASP cc_start: 0.7545 (p0) cc_final: 0.7336 (p0) REVERT: B 312 ASP cc_start: 0.8278 (m-30) cc_final: 0.7999 (m-30) REVERT: G 21 MET cc_start: 0.7174 (tpt) cc_final: 0.6694 (ttp) REVERT: N 3 GLN cc_start: 0.7288 (tp40) cc_final: 0.6468 (tm-30) REVERT: N 31 ASN cc_start: 0.7938 (m-40) cc_final: 0.7691 (t0) REVERT: N 77 ASN cc_start: 0.7551 (m-40) cc_final: 0.7238 (p0) REVERT: R 136 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7166 (p) REVERT: R 142 LEU cc_start: 0.8305 (tp) cc_final: 0.8034 (tm) REVERT: R 144 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7534 (tp) REVERT: R 148 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5614 (p90) REVERT: R 197 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7718 (tmmm) REVERT: R 262 GLU cc_start: 0.8326 (pt0) cc_final: 0.7912 (pt0) REVERT: R 292 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7300 (mm-30) REVERT: R 346 LYS cc_start: 0.7558 (mttt) cc_final: 0.6956 (pttm) REVERT: R 383 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8330 (tmtp) REVERT: R 423 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6876 (pt0) outliers start: 30 outliers final: 5 residues processed: 301 average time/residue: 1.1648 time to fit residues: 372.7119 Evaluate side-chains 162 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 421 ARG Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 41 HIS A 220 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 35 ASN R 171 HIS R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8656 Z= 0.294 Angle : 0.637 7.427 11758 Z= 0.334 Chirality : 0.045 0.154 1325 Planarity : 0.005 0.047 1454 Dihedral : 8.449 61.870 1555 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.26 % Allowed : 20.07 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1019 helix: -0.08 (0.25), residues: 395 sheet: -0.65 (0.33), residues: 217 loop : -1.00 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.019 0.002 PHE A 273 TYR 0.027 0.002 TYR R 148 ARG 0.007 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7942 (tp40) cc_final: 0.7720 (tp-100) REVERT: A 215 ASP cc_start: 0.7687 (t0) cc_final: 0.7100 (t0) REVERT: A 296 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (tm) REVERT: A 325 THR cc_start: 0.8869 (m) cc_final: 0.8558 (p) REVERT: A 343 ASP cc_start: 0.7953 (m-30) cc_final: 0.7529 (m-30) REVERT: A 372 ILE cc_start: 0.8821 (mp) cc_final: 0.8575 (mp) REVERT: A 378 ASP cc_start: 0.7194 (m-30) cc_final: 0.6871 (m-30) REVERT: B 38 ASP cc_start: 0.8471 (p0) cc_final: 0.7851 (p0) REVERT: B 44 GLN cc_start: 0.7928 (pt0) cc_final: 0.7625 (pt0) REVERT: B 132 ASN cc_start: 0.6716 (p0) cc_final: 0.6190 (p0) REVERT: B 134 ARG cc_start: 0.7678 (ptp90) cc_final: 0.7165 (ptp90) REVERT: B 135 VAL cc_start: 0.8809 (t) cc_final: 0.8556 (p) REVERT: B 138 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7719 (mt-10) REVERT: B 243 THR cc_start: 0.7544 (p) cc_final: 0.7145 (p) REVERT: G 29 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8132 (tppt) REVERT: G 38 MET cc_start: 0.7398 (ptp) cc_final: 0.6992 (ttp) REVERT: G 42 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7053 (mp0) REVERT: N 3 GLN cc_start: 0.7364 (tp40) cc_final: 0.6629 (tm-30) REVERT: N 31 ASN cc_start: 0.8242 (m110) cc_final: 0.7924 (m-40) REVERT: N 35 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8254 (p0) REVERT: N 77 ASN cc_start: 0.7353 (m-40) cc_final: 0.7031 (p0) REVERT: N 120 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8387 (tp40) REVERT: R 139 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8329 (tt0) REVERT: R 142 LEU cc_start: 0.8341 (tp) cc_final: 0.8032 (tm) REVERT: R 170 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8113 (tpp-160) REVERT: R 262 GLU cc_start: 0.8110 (pt0) cc_final: 0.7754 (pt0) REVERT: R 346 LYS cc_start: 0.7530 (mttt) cc_final: 0.6949 (pttm) REVERT: R 387 GLU cc_start: 0.8337 (tt0) cc_final: 0.7406 (mt-10) REVERT: R 394 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: R 397 MET cc_start: 0.7547 (mmt) cc_final: 0.7242 (mmt) REVERT: R 407 ASN cc_start: 0.8908 (m-40) cc_final: 0.8622 (m-40) REVERT: R 412 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7703 (tm-30) REVERT: R 423 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6202 (tm-30) outliers start: 38 outliers final: 13 residues processed: 194 average time/residue: 1.1712 time to fit residues: 241.9467 Evaluate side-chains 158 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 90 optimal weight: 0.0470 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8656 Z= 0.194 Angle : 0.568 7.202 11758 Z= 0.298 Chirality : 0.042 0.149 1325 Planarity : 0.004 0.043 1454 Dihedral : 7.102 58.233 1529 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.26 % Allowed : 21.97 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1019 helix: 0.52 (0.26), residues: 396 sheet: -0.41 (0.34), residues: 218 loop : -0.84 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.030 0.002 PHE N 27 TYR 0.020 0.002 TYR R 148 ARG 0.008 0.001 ARG R 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7890 (tp40) cc_final: 0.7670 (tp-100) REVERT: A 34 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8291 (tttp) REVERT: A 213 GLN cc_start: 0.8594 (tt0) cc_final: 0.8061 (tt0) REVERT: A 215 ASP cc_start: 0.7600 (t0) cc_final: 0.7039 (t0) REVERT: A 325 THR cc_start: 0.8886 (m) cc_final: 0.8589 (p) REVERT: A 343 ASP cc_start: 0.7998 (m-30) cc_final: 0.7625 (m-30) REVERT: A 357 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8201 (p90) REVERT: A 372 ILE cc_start: 0.8879 (mp) cc_final: 0.8603 (mp) REVERT: B 38 ASP cc_start: 0.8448 (p0) cc_final: 0.7848 (p0) REVERT: B 44 GLN cc_start: 0.7927 (pt0) cc_final: 0.7615 (pt0) REVERT: B 124 TYR cc_start: 0.8052 (m-80) cc_final: 0.7845 (m-80) REVERT: B 132 ASN cc_start: 0.6908 (p0) cc_final: 0.6322 (p0) REVERT: B 134 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7226 (ptp90) REVERT: B 135 VAL cc_start: 0.8869 (t) cc_final: 0.8669 (p) REVERT: B 138 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 215 GLU cc_start: 0.7818 (mp0) cc_final: 0.7402 (mp0) REVERT: B 226 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 228 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: B 243 THR cc_start: 0.7475 (p) cc_final: 0.7063 (p) REVERT: G 20 LYS cc_start: 0.7333 (ttpp) cc_final: 0.6978 (tmmt) REVERT: G 21 MET cc_start: 0.7108 (ttp) cc_final: 0.6474 (ttp) REVERT: G 38 MET cc_start: 0.7351 (ptp) cc_final: 0.6967 (ttp) REVERT: G 42 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7264 (mp0) REVERT: N 3 GLN cc_start: 0.7329 (tp40) cc_final: 0.6689 (tm-30) REVERT: N 31 ASN cc_start: 0.8218 (m110) cc_final: 0.7932 (t0) REVERT: N 67 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.4226 (ptm-80) REVERT: N 77 ASN cc_start: 0.7200 (m-40) cc_final: 0.6829 (p0) REVERT: N 90 ASP cc_start: 0.8224 (m-30) cc_final: 0.8024 (m-30) REVERT: N 110 VAL cc_start: 0.8674 (m) cc_final: 0.8354 (t) REVERT: N 120 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8305 (tp40) REVERT: R 139 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8385 (tt0) REVERT: R 142 LEU cc_start: 0.8273 (tp) cc_final: 0.8011 (tm) REVERT: R 170 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8110 (mtp85) REVERT: R 262 GLU cc_start: 0.8028 (pt0) cc_final: 0.7711 (pt0) REVERT: R 302 ASN cc_start: 0.9005 (t0) cc_final: 0.8568 (t0) REVERT: R 346 LYS cc_start: 0.7486 (mttt) cc_final: 0.6914 (pttm) REVERT: R 394 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: R 412 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7606 (tm-30) outliers start: 38 outliers final: 15 residues processed: 181 average time/residue: 1.0931 time to fit residues: 211.3180 Evaluate side-chains 165 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 239 ASN B 230 ASN B 340 ASN G 44 HIS G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8656 Z= 0.260 Angle : 0.563 7.271 11758 Z= 0.296 Chirality : 0.043 0.150 1325 Planarity : 0.004 0.056 1454 Dihedral : 6.961 57.969 1529 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.38 % Allowed : 22.09 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1019 helix: 0.79 (0.26), residues: 408 sheet: -0.33 (0.33), residues: 223 loop : -0.71 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.011 0.001 HIS A 357 PHE 0.024 0.002 PHE N 27 TYR 0.016 0.002 TYR R 148 ARG 0.011 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7632 (t0) cc_final: 0.7076 (t0) REVERT: A 325 THR cc_start: 0.8934 (m) cc_final: 0.8635 (p) REVERT: A 343 ASP cc_start: 0.8046 (m-30) cc_final: 0.7688 (m-30) REVERT: A 378 ASP cc_start: 0.7446 (m-30) cc_final: 0.7074 (m-30) REVERT: B 38 ASP cc_start: 0.8457 (p0) cc_final: 0.7871 (p0) REVERT: B 44 GLN cc_start: 0.8071 (pt0) cc_final: 0.7722 (pt0) REVERT: B 132 ASN cc_start: 0.7015 (p0) cc_final: 0.6245 (p0) REVERT: B 134 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7228 (ptp90) REVERT: B 138 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 215 GLU cc_start: 0.7847 (mp0) cc_final: 0.7401 (mp0) REVERT: B 228 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: B 243 THR cc_start: 0.7501 (p) cc_final: 0.7056 (p) REVERT: G 21 MET cc_start: 0.7048 (ttp) cc_final: 0.6494 (ttp) REVERT: G 38 MET cc_start: 0.7510 (ptp) cc_final: 0.5640 (ttp) REVERT: G 42 GLU cc_start: 0.7893 (mt-10) cc_final: 0.6952 (mp0) REVERT: N 3 GLN cc_start: 0.7370 (tp40) cc_final: 0.6750 (tm-30) REVERT: N 31 ASN cc_start: 0.8363 (m110) cc_final: 0.8032 (m-40) REVERT: N 105 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7534 (ttp-110) REVERT: N 110 VAL cc_start: 0.8580 (m) cc_final: 0.8304 (t) REVERT: N 117 TYR cc_start: 0.7478 (m-80) cc_final: 0.7068 (m-80) REVERT: N 120 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8246 (tp40) REVERT: R 139 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8342 (tt0) REVERT: R 142 LEU cc_start: 0.8271 (tp) cc_final: 0.8012 (tm) REVERT: R 170 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (mtp85) REVERT: R 197 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7957 (tppt) REVERT: R 203 TRP cc_start: 0.7216 (t-100) cc_final: 0.7009 (t-100) REVERT: R 326 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7358 (tpt-90) REVERT: R 346 LYS cc_start: 0.7443 (mttt) cc_final: 0.6783 (pttm) REVERT: R 394 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7837 (tt0) outliers start: 48 outliers final: 20 residues processed: 189 average time/residue: 1.1833 time to fit residues: 238.3052 Evaluate side-chains 174 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8656 Z= 0.213 Angle : 0.556 8.363 11758 Z= 0.286 Chirality : 0.042 0.153 1325 Planarity : 0.004 0.041 1454 Dihedral : 6.731 57.580 1526 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.15 % Allowed : 24.89 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1019 helix: 1.03 (0.27), residues: 399 sheet: -0.37 (0.33), residues: 223 loop : -0.56 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 277 HIS 0.003 0.001 HIS B 225 PHE 0.039 0.002 PHE N 27 TYR 0.017 0.001 TYR R 148 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7539 (t0) cc_final: 0.6979 (t0) REVERT: A 325 THR cc_start: 0.8889 (m) cc_final: 0.8591 (p) REVERT: A 343 ASP cc_start: 0.8032 (m-30) cc_final: 0.7664 (m-30) REVERT: A 378 ASP cc_start: 0.7437 (m-30) cc_final: 0.7049 (m-30) REVERT: B 38 ASP cc_start: 0.8471 (p0) cc_final: 0.7898 (p0) REVERT: B 132 ASN cc_start: 0.6977 (p0) cc_final: 0.5996 (p0) REVERT: B 134 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7153 (ptp90) REVERT: B 135 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8662 (p) REVERT: B 138 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 215 GLU cc_start: 0.7916 (mp0) cc_final: 0.7572 (mp0) REVERT: B 217 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7932 (pmm) REVERT: B 228 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: B 243 THR cc_start: 0.7600 (p) cc_final: 0.7171 (p) REVERT: G 21 MET cc_start: 0.7029 (ttp) cc_final: 0.6322 (ttp) REVERT: G 38 MET cc_start: 0.7562 (ptp) cc_final: 0.6988 (ttp) REVERT: G 42 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7235 (mp0) REVERT: N 3 GLN cc_start: 0.7361 (tp40) cc_final: 0.6781 (tm-30) REVERT: N 31 ASN cc_start: 0.8278 (m110) cc_final: 0.7999 (t0) REVERT: N 105 ARG cc_start: 0.7845 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: N 110 VAL cc_start: 0.8614 (m) cc_final: 0.8338 (t) REVERT: N 120 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8210 (tp40) REVERT: R 139 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8356 (tt0) REVERT: R 142 LEU cc_start: 0.8243 (tp) cc_final: 0.7986 (tm) REVERT: R 170 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8040 (tpp-160) REVERT: R 302 ASN cc_start: 0.8952 (t0) cc_final: 0.8445 (t0) REVERT: R 326 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7378 (tpt-90) REVERT: R 346 LYS cc_start: 0.7447 (mttt) cc_final: 0.6790 (pttm) REVERT: R 394 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7853 (tt0) outliers start: 37 outliers final: 17 residues processed: 181 average time/residue: 1.1141 time to fit residues: 215.8000 Evaluate side-chains 172 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8656 Z= 0.247 Angle : 0.571 7.333 11758 Z= 0.293 Chirality : 0.042 0.147 1325 Planarity : 0.004 0.045 1454 Dihedral : 6.708 58.595 1526 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.71 % Allowed : 26.12 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 1019 helix: 1.17 (0.26), residues: 397 sheet: -0.43 (0.33), residues: 224 loop : -0.43 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 277 HIS 0.004 0.001 HIS R 363 PHE 0.055 0.002 PHE N 27 TYR 0.019 0.002 TYR N 32 ARG 0.012 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7586 (t0) cc_final: 0.7026 (t0) REVERT: A 325 THR cc_start: 0.8868 (m) cc_final: 0.8578 (p) REVERT: A 343 ASP cc_start: 0.8032 (m-30) cc_final: 0.7646 (m-30) REVERT: A 378 ASP cc_start: 0.7588 (m-30) cc_final: 0.7228 (m-30) REVERT: A 392 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: B 38 ASP cc_start: 0.8487 (p0) cc_final: 0.7940 (p0) REVERT: B 132 ASN cc_start: 0.6960 (p0) cc_final: 0.5940 (p0) REVERT: B 134 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7190 (ptp90) REVERT: B 138 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 215 GLU cc_start: 0.7918 (mp0) cc_final: 0.7650 (mp0) REVERT: B 217 MET cc_start: 0.8370 (ptt) cc_final: 0.7916 (pmm) REVERT: B 228 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: B 243 THR cc_start: 0.7466 (p) cc_final: 0.7198 (p) REVERT: G 21 MET cc_start: 0.7023 (ttp) cc_final: 0.6212 (ttp) REVERT: G 38 MET cc_start: 0.7617 (ptp) cc_final: 0.7048 (ttp) REVERT: G 42 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7223 (mp0) REVERT: N 3 GLN cc_start: 0.7335 (tp40) cc_final: 0.6716 (tm-30) REVERT: N 31 ASN cc_start: 0.8264 (m110) cc_final: 0.7959 (t0) REVERT: N 110 VAL cc_start: 0.8586 (m) cc_final: 0.8320 (t) REVERT: N 117 TYR cc_start: 0.7376 (m-80) cc_final: 0.7037 (m-80) REVERT: N 120 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8132 (tp40) REVERT: R 139 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8316 (tt0) REVERT: R 142 LEU cc_start: 0.8330 (tp) cc_final: 0.8035 (tm) REVERT: R 146 ILE cc_start: 0.6698 (tt) cc_final: 0.6394 (tp) REVERT: R 170 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8100 (tpp-160) REVERT: R 262 GLU cc_start: 0.8136 (pt0) cc_final: 0.7880 (pm20) REVERT: R 302 ASN cc_start: 0.8678 (t0) cc_final: 0.8430 (t0) REVERT: R 326 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7371 (tpt-90) REVERT: R 346 LYS cc_start: 0.7462 (mttt) cc_final: 0.6803 (pttm) REVERT: R 394 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: R 414 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6375 (mpt180) outliers start: 42 outliers final: 24 residues processed: 186 average time/residue: 1.1962 time to fit residues: 237.2367 Evaluate side-chains 183 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8656 Z= 0.247 Angle : 0.582 8.842 11758 Z= 0.297 Chirality : 0.042 0.147 1325 Planarity : 0.004 0.048 1454 Dihedral : 6.669 56.250 1526 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.71 % Allowed : 26.57 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 1019 helix: 1.11 (0.26), residues: 403 sheet: -0.43 (0.32), residues: 220 loop : -0.47 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 277 HIS 0.003 0.001 HIS R 180 PHE 0.066 0.002 PHE N 27 TYR 0.016 0.002 TYR N 32 ARG 0.011 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7564 (mpt) cc_final: 0.7201 (mpt) REVERT: A 215 ASP cc_start: 0.7574 (t0) cc_final: 0.7014 (t0) REVERT: A 325 THR cc_start: 0.8868 (m) cc_final: 0.8570 (p) REVERT: A 343 ASP cc_start: 0.8036 (m-30) cc_final: 0.7637 (m-30) REVERT: A 378 ASP cc_start: 0.7568 (m-30) cc_final: 0.7193 (m-30) REVERT: A 392 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: B 38 ASP cc_start: 0.8599 (p0) cc_final: 0.8085 (p0) REVERT: B 132 ASN cc_start: 0.7014 (p0) cc_final: 0.5907 (p0) REVERT: B 134 ARG cc_start: 0.7618 (ptp90) cc_final: 0.7080 (ptp90) REVERT: B 138 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 215 GLU cc_start: 0.7895 (mp0) cc_final: 0.7672 (mp0) REVERT: B 217 MET cc_start: 0.8410 (ptt) cc_final: 0.8038 (pmm) REVERT: B 226 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 228 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: B 243 THR cc_start: 0.7484 (p) cc_final: 0.7116 (p) REVERT: G 21 MET cc_start: 0.7016 (ttp) cc_final: 0.6178 (ttp) REVERT: G 38 MET cc_start: 0.7649 (ptp) cc_final: 0.7016 (ttp) REVERT: G 42 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7220 (mp0) REVERT: N 3 GLN cc_start: 0.7323 (tp40) cc_final: 0.6692 (tm-30) REVERT: N 31 ASN cc_start: 0.8206 (m110) cc_final: 0.7886 (t0) REVERT: N 110 VAL cc_start: 0.8602 (m) cc_final: 0.8353 (t) REVERT: N 120 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8224 (tp40) REVERT: R 139 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8357 (tt0) REVERT: R 142 LEU cc_start: 0.8350 (tp) cc_final: 0.7897 (tm) REVERT: R 260 LEU cc_start: 0.8141 (pt) cc_final: 0.7915 (mm) REVERT: R 262 GLU cc_start: 0.8165 (pt0) cc_final: 0.7893 (pm20) REVERT: R 299 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: R 302 ASN cc_start: 0.8777 (t0) cc_final: 0.8283 (t0) REVERT: R 326 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7354 (tpt-90) REVERT: R 346 LYS cc_start: 0.7523 (mttt) cc_final: 0.6864 (pttm) REVERT: R 394 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: R 414 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6350 (mpt180) outliers start: 42 outliers final: 26 residues processed: 187 average time/residue: 1.1381 time to fit residues: 227.9740 Evaluate side-chains 185 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8656 Z= 0.213 Angle : 0.571 7.744 11758 Z= 0.293 Chirality : 0.042 0.146 1325 Planarity : 0.004 0.051 1454 Dihedral : 6.541 55.226 1526 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.04 % Allowed : 27.24 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 1019 helix: 1.40 (0.27), residues: 391 sheet: -0.33 (0.32), residues: 220 loop : -0.36 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 277 HIS 0.002 0.001 HIS A 220 PHE 0.033 0.001 PHE N 27 TYR 0.017 0.001 TYR B 124 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8002 (mpt) cc_final: 0.7639 (mpt) REVERT: A 215 ASP cc_start: 0.7493 (t0) cc_final: 0.6972 (t0) REVERT: A 292 ASN cc_start: 0.8285 (t0) cc_final: 0.7933 (p0) REVERT: A 295 ASP cc_start: 0.8870 (p0) cc_final: 0.8597 (m-30) REVERT: A 325 THR cc_start: 0.8861 (m) cc_final: 0.8565 (p) REVERT: A 343 ASP cc_start: 0.8040 (m-30) cc_final: 0.7634 (m-30) REVERT: A 378 ASP cc_start: 0.7695 (m-30) cc_final: 0.7343 (m-30) REVERT: A 392 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: B 13 GLN cc_start: 0.7970 (mm110) cc_final: 0.7727 (mm110) REVERT: B 38 ASP cc_start: 0.8601 (p0) cc_final: 0.8084 (p0) REVERT: B 132 ASN cc_start: 0.6996 (p0) cc_final: 0.5845 (p0) REVERT: B 134 ARG cc_start: 0.7718 (ptp90) cc_final: 0.7183 (ptp90) REVERT: B 138 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 215 GLU cc_start: 0.7873 (mp0) cc_final: 0.7612 (mp0) REVERT: B 217 MET cc_start: 0.8410 (ptt) cc_final: 0.8040 (pmm) REVERT: B 226 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 228 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: B 243 THR cc_start: 0.7456 (p) cc_final: 0.7062 (p) REVERT: G 21 MET cc_start: 0.7014 (ttp) cc_final: 0.6208 (ttp) REVERT: G 38 MET cc_start: 0.7631 (ptp) cc_final: 0.6851 (ttp) REVERT: G 42 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7141 (mp0) REVERT: G 47 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6920 (mp0) REVERT: N 3 GLN cc_start: 0.7289 (tp40) cc_final: 0.6633 (tm-30) REVERT: N 27 PHE cc_start: 0.6637 (p90) cc_final: 0.6185 (p90) REVERT: N 110 VAL cc_start: 0.8598 (m) cc_final: 0.8338 (t) REVERT: N 120 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8203 (tp40) REVERT: R 139 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8327 (tt0) REVERT: R 142 LEU cc_start: 0.8213 (tp) cc_final: 0.7960 (tm) REVERT: R 148 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6762 (p90) REVERT: R 260 LEU cc_start: 0.8163 (pt) cc_final: 0.7918 (mm) REVERT: R 262 GLU cc_start: 0.8135 (pt0) cc_final: 0.7890 (pm20) REVERT: R 299 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: R 326 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7385 (tpt-90) REVERT: R 346 LYS cc_start: 0.7531 (mttt) cc_final: 0.6858 (pttm) REVERT: R 394 GLN cc_start: 0.8214 (pt0) cc_final: 0.7850 (tt0) REVERT: R 414 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6276 (mpt180) outliers start: 36 outliers final: 25 residues processed: 182 average time/residue: 1.1786 time to fit residues: 228.4531 Evaluate side-chains 185 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8656 Z= 0.210 Angle : 0.579 10.229 11758 Z= 0.297 Chirality : 0.041 0.145 1325 Planarity : 0.004 0.055 1454 Dihedral : 6.499 54.258 1526 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.81 % Allowed : 28.14 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1019 helix: 1.37 (0.27), residues: 395 sheet: -0.32 (0.32), residues: 222 loop : -0.33 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 277 HIS 0.002 0.001 HIS A 220 PHE 0.044 0.002 PHE N 27 TYR 0.031 0.002 TYR R 305 ARG 0.014 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8290 (pp20) cc_final: 0.7877 (pp20) REVERT: A 60 MET cc_start: 0.7953 (mpt) cc_final: 0.7585 (mpt) REVERT: A 215 ASP cc_start: 0.7490 (t0) cc_final: 0.6969 (t0) REVERT: A 292 ASN cc_start: 0.8243 (t0) cc_final: 0.8002 (p0) REVERT: A 295 ASP cc_start: 0.8886 (p0) cc_final: 0.8620 (m-30) REVERT: A 296 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8475 (tm) REVERT: A 325 THR cc_start: 0.8854 (m) cc_final: 0.8550 (p) REVERT: A 343 ASP cc_start: 0.8017 (m-30) cc_final: 0.7644 (m-30) REVERT: A 378 ASP cc_start: 0.7668 (m-30) cc_final: 0.7326 (m-30) REVERT: A 392 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: B 13 GLN cc_start: 0.7940 (mm110) cc_final: 0.7710 (mm110) REVERT: B 37 ILE cc_start: 0.8053 (pp) cc_final: 0.7799 (pp) REVERT: B 38 ASP cc_start: 0.8603 (p0) cc_final: 0.8107 (p0) REVERT: B 132 ASN cc_start: 0.7119 (p0) cc_final: 0.6052 (p0) REVERT: B 134 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7089 (ptp90) REVERT: B 138 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 214 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7739 (mtt90) REVERT: B 215 GLU cc_start: 0.7829 (mp0) cc_final: 0.7582 (mp0) REVERT: B 217 MET cc_start: 0.8412 (ptt) cc_final: 0.8059 (pmm) REVERT: B 226 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7513 (mt-10) REVERT: B 228 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 243 THR cc_start: 0.7515 (p) cc_final: 0.7122 (p) REVERT: G 21 MET cc_start: 0.7070 (ttp) cc_final: 0.6176 (ttp) REVERT: G 38 MET cc_start: 0.7624 (ptp) cc_final: 0.6841 (ttp) REVERT: G 42 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7137 (mp0) REVERT: G 47 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6905 (mp0) REVERT: N 3 GLN cc_start: 0.7206 (tp40) cc_final: 0.6518 (tm-30) REVERT: N 31 ASN cc_start: 0.8230 (m110) cc_final: 0.7866 (t0) REVERT: N 110 VAL cc_start: 0.8630 (m) cc_final: 0.8386 (t) REVERT: R 139 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8346 (tt0) REVERT: R 148 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6567 (p90) REVERT: R 260 LEU cc_start: 0.8155 (pt) cc_final: 0.7930 (mm) REVERT: R 262 GLU cc_start: 0.8144 (pt0) cc_final: 0.7887 (pm20) REVERT: R 299 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7540 (ttm170) REVERT: R 326 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7405 (tpt-90) REVERT: R 388 LEU cc_start: 0.8219 (mm) cc_final: 0.7870 (mt) REVERT: R 394 GLN cc_start: 0.8244 (pt0) cc_final: 0.7788 (tt0) REVERT: R 414 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6445 (mmp-170) REVERT: R 418 GLU cc_start: 0.6566 (pp20) cc_final: 0.6153 (pp20) outliers start: 34 outliers final: 21 residues processed: 184 average time/residue: 1.2851 time to fit residues: 251.4618 Evaluate side-chains 181 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8656 Z= 0.231 Angle : 0.604 9.062 11758 Z= 0.310 Chirality : 0.042 0.181 1325 Planarity : 0.004 0.061 1454 Dihedral : 6.499 53.490 1526 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 28.92 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1019 helix: 1.32 (0.26), residues: 395 sheet: -0.33 (0.32), residues: 222 loop : -0.35 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 277 HIS 0.002 0.001 HIS R 180 PHE 0.021 0.001 PHE N 27 TYR 0.019 0.002 TYR B 124 ARG 0.015 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8026 (mpt) cc_final: 0.7631 (mpt) REVERT: A 215 ASP cc_start: 0.7546 (t0) cc_final: 0.7024 (t0) REVERT: A 295 ASP cc_start: 0.8893 (p0) cc_final: 0.8654 (m-30) REVERT: A 296 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (tm) REVERT: A 325 THR cc_start: 0.8866 (m) cc_final: 0.8566 (p) REVERT: A 343 ASP cc_start: 0.8043 (m-30) cc_final: 0.7631 (m-30) REVERT: A 378 ASP cc_start: 0.7686 (m-30) cc_final: 0.7382 (m-30) REVERT: A 392 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: B 13 GLN cc_start: 0.7939 (mm110) cc_final: 0.7706 (mm110) REVERT: B 37 ILE cc_start: 0.8116 (pp) cc_final: 0.7865 (pp) REVERT: B 38 ASP cc_start: 0.8604 (p0) cc_final: 0.8129 (p0) REVERT: B 132 ASN cc_start: 0.7171 (p0) cc_final: 0.6037 (p0) REVERT: B 134 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7034 (ptp90) REVERT: B 138 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 215 GLU cc_start: 0.7872 (mp0) cc_final: 0.7582 (mp0) REVERT: B 217 MET cc_start: 0.8422 (ptt) cc_final: 0.8056 (pmm) REVERT: B 228 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: B 243 THR cc_start: 0.7528 (p) cc_final: 0.7139 (p) REVERT: G 17 GLU cc_start: 0.7039 (tp30) cc_final: 0.6286 (mp0) REVERT: G 21 MET cc_start: 0.7213 (ttp) cc_final: 0.6230 (ttp) REVERT: G 38 MET cc_start: 0.7624 (ptp) cc_final: 0.6843 (ttp) REVERT: G 42 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7139 (mp0) REVERT: N 3 GLN cc_start: 0.7267 (tp40) cc_final: 0.6550 (tm-30) REVERT: N 31 ASN cc_start: 0.8288 (m110) cc_final: 0.7893 (m-40) REVERT: N 84 ASN cc_start: 0.8141 (m-40) cc_final: 0.7883 (m-40) REVERT: N 110 VAL cc_start: 0.8623 (m) cc_final: 0.8374 (t) REVERT: N 120 GLN cc_start: 0.8713 (tp40) cc_final: 0.8379 (tp40) REVERT: R 139 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8349 (tt0) REVERT: R 148 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6602 (p90) REVERT: R 262 GLU cc_start: 0.8144 (pt0) cc_final: 0.7815 (pm20) REVERT: R 299 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7534 (ttm170) REVERT: R 326 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7389 (tpt-90) REVERT: R 346 LYS cc_start: 0.7541 (mttt) cc_final: 0.6800 (ptpp) REVERT: R 388 LEU cc_start: 0.8210 (mm) cc_final: 0.7878 (mt) REVERT: R 394 GLN cc_start: 0.8214 (pt0) cc_final: 0.7836 (tt0) outliers start: 31 outliers final: 21 residues processed: 181 average time/residue: 1.1410 time to fit residues: 220.1790 Evaluate side-chains 182 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096244 restraints weight = 13103.773| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.83 r_work: 0.3182 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8656 Z= 0.221 Angle : 0.596 7.907 11758 Z= 0.308 Chirality : 0.042 0.146 1325 Planarity : 0.005 0.062 1454 Dihedral : 6.448 52.706 1526 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.14 % Allowed : 29.60 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1019 helix: 1.39 (0.27), residues: 395 sheet: -0.34 (0.33), residues: 222 loop : -0.30 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 264 HIS 0.002 0.001 HIS R 180 PHE 0.026 0.001 PHE R 385 TYR 0.021 0.001 TYR B 124 ARG 0.014 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.52 seconds wall clock time: 74 minutes 56.59 seconds (4496.59 seconds total)