Starting phenix.real_space_refine on Mon Dec 30 01:08:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmy_34904/12_2024/8hmy_34904.cif" } resolution = 2.94 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= 0.009 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 90 5.49 5 Mg 6 5.21 5 S 31 5.16 5 C 7001 2.51 5 N 2105 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11675 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2608 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 2 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2057 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain breaks: 1 Chain: "T" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1888 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 17, 'rna3p': 72} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan2': 1, ' G%rna2p_pur:plan2': 1, ' G%rna2p_pur:plan': 1, ' C%rna3p_pyr:plan2': 1, ' G%rna3p_pur:plan': 1, ' U%rna2p_pyr:plan': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2263 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 18, 'TRANS': 266} Chain breaks: 1 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1869 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 361} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1202 Unresolved non-hydrogen angles: 1543 Unresolved non-hydrogen dihedrals: 992 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 9, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 21, 'GLU:plan': 28, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 664 Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 8.59, per 1000 atoms: 0.74 Number of scatterers: 11675 At special positions: 0 Unit cell: (128.266, 119.57, 152.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 90 15.00 Mg 6 11.99 O 2442 8.00 N 2105 7.00 C 7001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 35.3% alpha, 20.2% beta 26 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 100 through 118 removed outlier: 4.383A pdb=" N ALA A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A 114 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.898A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.676A pdb=" N LEU A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.719A pdb=" N THR A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.930A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.922A pdb=" N VAL B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 79 through 112 removed outlier: 3.523A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 214 through 230 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'C' and resid 19 through 28 removed outlier: 3.588A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 66 removed outlier: 3.531A pdb=" N LEU C 62 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.615A pdb=" N GLN C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 101 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.531A pdb=" N LEU C 145 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.582A pdb=" N TYR C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.883A pdb=" N VAL C 176 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.642A pdb=" N GLU C 441 " --> pdb=" O ARG C 438 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS C 442 " --> pdb=" O LEU C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.535A pdb=" N ALA C 459 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 496 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'E' and resid 89 through 110 Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 192 through 195 Processing helix chain 'E' and resid 196 through 218 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 236 through 249 Processing helix chain 'E' and resid 259 through 270 Processing helix chain 'E' and resid 289 through 307 Processing helix chain 'E' and resid 308 through 311 removed outlier: 3.642A pdb=" N CYS E 311 " --> pdb=" O PHE E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 308 through 311' Processing helix chain 'E' and resid 322 through 324 No H-bonds generated for 'chain 'E' and resid 322 through 324' Processing helix chain 'E' and resid 358 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 4.162A pdb=" N VAL A 49 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.822A pdb=" N VAL A 260 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.486A pdb=" N LEU A 366 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 381 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 368 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 379 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET A 419 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER A 381 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 421 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 383 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 423 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A 385 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS A 425 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 387 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 418 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 451 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 512 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE C 515 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU C 500 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 505 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 471 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP C 451 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C 473 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.338A pdb=" N SER B 11 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 5 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 2 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL B 69 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 4 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 187 removed outlier: 4.176A pdb=" N ARG C 70 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 195 through 197 removed outlier: 3.773A pdb=" N VAL B 195 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.765A pdb=" N TYR B 258 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE B 259 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS B 291 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 261 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 288 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 303 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR D 104 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 142 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE D 90 " --> pdb=" O PRO D 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 95 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU D 78 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.620A pdb=" N ILE B 269 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 114 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.570A pdb=" N VAL C 78 " --> pdb=" O HIS C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 17 removed outlier: 6.409A pdb=" N SER E 72 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.576A pdb=" N THR E 21 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 81 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.458A pdb=" N THR E 146 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN E 229 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 148 " --> pdb=" O ASN E 229 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 117 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG E 116 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL E 255 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 118 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 257 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL E 120 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 315 through 320 removed outlier: 3.559A pdb=" N SER E 391 " --> pdb=" O THR E 400 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU E 402 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL E 389 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 385 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 364 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 365 " --> pdb=" O MET E 417 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS E 325 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE E 416 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR E 327 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASP E 418 " --> pdb=" O TYR E 327 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1749 1.29 - 1.42: 3556 1.42 - 1.55: 6534 1.55 - 1.68: 182 1.68 - 1.81: 50 Bond restraints: 12071 Sorted by residual: bond pdb=" CG ASP C 523 " pdb=" OD1 ASP C 523 " ideal model delta sigma weight residual 1.249 1.166 0.083 1.90e-02 2.77e+03 1.89e+01 bond pdb=" C VAL C 524 " pdb=" O VAL C 524 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.19e-02 7.06e+03 1.76e+01 bond pdb=" N PRO C 411 " pdb=" CD PRO C 411 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N GLU A 17 " pdb=" CA GLU A 17 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" C ASP C 523 " pdb=" O ASP C 523 " ideal model delta sigma weight residual 1.236 1.205 0.031 9.90e-03 1.02e+04 9.62e+00 ... (remaining 12066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16427 2.48 - 4.96: 383 4.96 - 7.45: 20 7.45 - 9.93: 6 9.93 - 12.41: 2 Bond angle restraints: 16838 Sorted by residual: angle pdb=" CA PRO C 411 " pdb=" N PRO C 411 " pdb=" CD PRO C 411 " ideal model delta sigma weight residual 112.00 99.59 12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" CA THR A 18 " pdb=" CB THR A 18 " pdb=" OG1 THR A 18 " ideal model delta sigma weight residual 109.60 99.47 10.13 1.50e+00 4.44e-01 4.56e+01 angle pdb=" N VAL C 426 " pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 113.53 107.57 5.96 9.80e-01 1.04e+00 3.69e+01 angle pdb=" N THR A 18 " pdb=" CA THR A 18 " pdb=" CB THR A 18 " ideal model delta sigma weight residual 110.49 118.96 -8.47 1.69e+00 3.50e-01 2.51e+01 angle pdb=" C VAL C 524 " pdb=" N GLY C 525 " pdb=" CA GLY C 525 " ideal model delta sigma weight residual 121.41 111.67 9.74 1.96e+00 2.60e-01 2.47e+01 ... (remaining 16833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6979 35.97 - 71.95: 370 71.95 - 107.92: 34 107.92 - 143.89: 0 143.89 - 179.87: 2 Dihedral angle restraints: 7385 sinusoidal: 3428 harmonic: 3957 Sorted by residual: dihedral pdb=" O4' C T 51 " pdb=" C1' C T 51 " pdb=" N1 C T 51 " pdb=" C2 C T 51 " ideal model delta sinusoidal sigma weight residual 232.00 52.13 179.87 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C THR A 18 " pdb=" N THR A 18 " pdb=" CA THR A 18 " pdb=" CB THR A 18 " ideal model delta harmonic sigma weight residual -122.00 -139.90 17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" N THR A 18 " pdb=" C THR A 18 " pdb=" CA THR A 18 " pdb=" CB THR A 18 " ideal model delta harmonic sigma weight residual 123.40 139.52 -16.12 0 2.50e+00 1.60e-01 4.16e+01 ... (remaining 7382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1963 0.128 - 0.256: 30 0.256 - 0.384: 4 0.384 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA THR A 18 " pdb=" N THR A 18 " pdb=" C THR A 18 " pdb=" CB THR A 18 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA GLU E 111 " pdb=" N GLU E 111 " pdb=" C GLU E 111 " pdb=" CB GLU E 111 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1997 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 522 " 0.024 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLN C 522 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN C 522 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP C 523 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 16 " 0.002 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR A 16 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 16 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 16 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 16 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR A 16 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 16 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 16 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 291 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C ASP E 291 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 291 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE E 292 " 0.017 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 348 2.69 - 3.24: 10323 3.24 - 3.79: 18039 3.79 - 4.35: 23406 4.35 - 4.90: 37743 Nonbonded interactions: 89859 Sorted by model distance: nonbonded pdb=" O2' U T 16 " pdb=" OP1 A T 19 " model vdw 2.137 3.040 nonbonded pdb=" OD2 ASP B 226 " pdb=" OH TYR B 301 " model vdw 2.154 3.040 nonbonded pdb=" OG SER B 303 " pdb=" O GLY D 158 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLU C 122 " pdb=" OH TYR C 155 " model vdw 2.175 3.040 nonbonded pdb=" O THR A 18 " pdb=" OG SER A 21 " model vdw 2.204 3.040 ... (remaining 89854 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.780 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.600 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 0.083 12071 Z= 0.349 Angle : 0.850 12.412 16838 Z= 0.537 Chirality : 0.053 0.639 2000 Planarity : 0.006 0.049 1872 Dihedral : 19.412 179.867 4823 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.28 % Rotamer: Outliers : 7.49 % Allowed : 25.06 % Favored : 67.45 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.35 (0.20), residues: 1346 helix: -1.07 (0.21), residues: 447 sheet: -0.97 (0.28), residues: 288 loop : -2.18 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS D 77 PHE 0.015 0.001 PHE A 391 TYR 0.044 0.002 TYR A 16 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6497 (t80) cc_final: 0.6268 (t80) REVERT: A 106 HIS cc_start: 0.4398 (OUTLIER) cc_final: 0.3997 (t-170) REVERT: A 283 ARG cc_start: 0.4324 (OUTLIER) cc_final: 0.2898 (ttp-170) REVERT: A 361 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8117 (mttm) REVERT: A 434 MET cc_start: 0.5913 (ttp) cc_final: 0.5455 (tpt) REVERT: A 435 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: D 47 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7161 (mt) REVERT: D 49 MET cc_start: 0.6114 (mtp) cc_final: 0.5677 (mtp) outliers start: 64 outliers final: 24 residues processed: 173 average time/residue: 1.2235 time to fit residues: 229.5495 Evaluate side-chains 127 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 161 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 46 ASN A 47 ASN A 106 HIS A 280 GLN A 390 HIS B 205 GLN B 272 GLN C 64 GLN C 69 GLN C 138 GLN C 413 GLN C 423 HIS D 117 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 12071 Z= 0.580 Angle : 0.795 8.578 16838 Z= 0.404 Chirality : 0.049 0.188 2000 Planarity : 0.006 0.051 1872 Dihedral : 18.406 175.421 2917 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 9.84 % Allowed : 26.58 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1346 helix: 0.04 (0.24), residues: 448 sheet: -0.62 (0.29), residues: 281 loop : -1.72 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 82 HIS 0.006 0.001 HIS C 160 PHE 0.021 0.003 PHE A 391 TYR 0.023 0.003 TYR C 513 ARG 0.007 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 97 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 106 HIS cc_start: 0.4709 (OUTLIER) cc_final: 0.4493 (t-170) REVERT: A 295 GLU cc_start: 0.4839 (OUTLIER) cc_final: 0.4565 (tp30) REVERT: A 350 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7793 (ttt-90) REVERT: A 401 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.6005 (m-10) REVERT: A 434 MET cc_start: 0.6013 (ttp) cc_final: 0.5462 (tpt) REVERT: B 223 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8704 (mt) REVERT: C 90 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: C 426 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6355 (p) REVERT: C 465 ASN cc_start: 0.7200 (t0) cc_final: 0.6862 (t0) REVERT: C 504 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7921 (mt) outliers start: 84 outliers final: 45 residues processed: 175 average time/residue: 1.1998 time to fit residues: 228.8237 Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 64 GLN C 413 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12071 Z= 0.162 Angle : 0.546 7.348 16838 Z= 0.282 Chirality : 0.041 0.185 2000 Planarity : 0.004 0.048 1872 Dihedral : 17.921 179.233 2900 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 7.61 % Allowed : 27.87 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.55 (0.22), residues: 1346 helix: 1.03 (0.25), residues: 443 sheet: -0.39 (0.29), residues: 282 loop : -1.38 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.015 0.001 HIS A 31 PHE 0.013 0.001 PHE A 391 TYR 0.012 0.001 TYR A 346 ARG 0.005 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 97 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6085 (mtt180) REVERT: A 61 TYR cc_start: 0.6752 (t80) cc_final: 0.6504 (t80) REVERT: A 95 ASN cc_start: 0.1205 (OUTLIER) cc_final: 0.0803 (m-40) REVERT: A 115 MET cc_start: 0.5106 (mtp) cc_final: 0.4683 (ptp) REVERT: A 401 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.6074 (m-10) REVERT: A 435 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6737 (pp20) REVERT: B 123 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6207 (mmpt) REVERT: B 223 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 426 VAL cc_start: 0.6531 (OUTLIER) cc_final: 0.6250 (p) REVERT: C 523 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7395 (t0) outliers start: 65 outliers final: 30 residues processed: 158 average time/residue: 1.1872 time to fit residues: 204.6598 Evaluate side-chains 131 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 138 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN B 294 GLN C 64 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 12071 Z= 0.571 Angle : 0.773 9.672 16838 Z= 0.388 Chirality : 0.049 0.186 2000 Planarity : 0.006 0.052 1872 Dihedral : 18.084 175.609 2885 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 9.25 % Allowed : 26.93 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.78 (0.22), residues: 1346 helix: 0.61 (0.24), residues: 455 sheet: -0.45 (0.30), residues: 280 loop : -1.39 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 82 HIS 0.006 0.001 HIS C 160 PHE 0.021 0.003 PHE A 391 TYR 0.021 0.003 TYR C 513 ARG 0.006 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 86 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6737 (t80) cc_final: 0.6496 (t80) REVERT: A 95 ASN cc_start: 0.1303 (OUTLIER) cc_final: 0.0854 (m-40) REVERT: A 115 MET cc_start: 0.5174 (mtp) cc_final: 0.4740 (ptp) REVERT: A 350 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7750 (ttt-90) REVERT: A 401 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: B 38 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7155 (ptm160) REVERT: B 123 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6191 (mmpt) REVERT: B 223 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 90 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: C 426 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.6426 (p) REVERT: C 465 ASN cc_start: 0.7151 (t0) cc_final: 0.6815 (t0) REVERT: C 504 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7932 (mt) REVERT: D 47 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6907 (mt) outliers start: 79 outliers final: 50 residues processed: 159 average time/residue: 1.2226 time to fit residues: 211.7189 Evaluate side-chains 144 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 84 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN C 64 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12071 Z= 0.370 Angle : 0.660 9.070 16838 Z= 0.334 Chirality : 0.044 0.187 2000 Planarity : 0.005 0.047 1872 Dihedral : 18.044 176.194 2885 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 8.20 % Allowed : 26.81 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1346 helix: 0.86 (0.25), residues: 454 sheet: -0.45 (0.30), residues: 280 loop : -1.32 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.004 0.001 HIS C 160 PHE 0.017 0.002 PHE A 391 TYR 0.021 0.002 TYR C 513 ARG 0.003 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 88 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6773 (t80) cc_final: 0.6455 (t80) REVERT: A 95 ASN cc_start: 0.1277 (OUTLIER) cc_final: 0.0853 (m-40) REVERT: A 115 MET cc_start: 0.5062 (mtp) cc_final: 0.4653 (ptp) REVERT: A 350 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7688 (ttt-90) REVERT: A 361 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7925 (mttm) REVERT: A 401 TRP cc_start: 0.7047 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: B 38 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7184 (ptm160) REVERT: B 123 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6203 (mmpt) REVERT: B 223 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 90 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (tp30) REVERT: C 504 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 523 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7007 (t0) REVERT: C 526 HIS cc_start: 0.2432 (OUTLIER) cc_final: 0.2188 (t-90) outliers start: 70 outliers final: 45 residues processed: 155 average time/residue: 1.2519 time to fit residues: 213.0565 Evaluate side-chains 140 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 84 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 526 HIS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN B 110 GLN C 64 GLN D 77 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12071 Z= 0.189 Angle : 0.546 8.755 16838 Z= 0.277 Chirality : 0.040 0.177 2000 Planarity : 0.004 0.044 1872 Dihedral : 17.800 179.754 2884 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 7.38 % Allowed : 27.40 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.23), residues: 1346 helix: 1.36 (0.25), residues: 452 sheet: -0.21 (0.30), residues: 281 loop : -1.17 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS D 77 PHE 0.016 0.001 PHE C 518 TYR 0.021 0.002 TYR A 309 ARG 0.007 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 90 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6660 (t80) cc_final: 0.6376 (t80) REVERT: A 90 LYS cc_start: 0.4982 (OUTLIER) cc_final: 0.3909 (mmtp) REVERT: A 95 ASN cc_start: 0.1167 (OUTLIER) cc_final: 0.0739 (m-40) REVERT: A 115 MET cc_start: 0.5078 (mtp) cc_final: 0.4688 (ptp) REVERT: A 361 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7839 (mttm) REVERT: A 401 TRP cc_start: 0.6837 (OUTLIER) cc_final: 0.6082 (m-10) REVERT: A 435 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7001 (pp20) REVERT: B 38 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6718 (ptm160) REVERT: B 123 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6129 (mmpt) REVERT: B 223 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 90 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 504 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7835 (mt) REVERT: C 523 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7455 (t0) REVERT: C 526 HIS cc_start: 0.2396 (OUTLIER) cc_final: 0.2094 (t-90) outliers start: 63 outliers final: 35 residues processed: 148 average time/residue: 1.2051 time to fit residues: 194.2363 Evaluate side-chains 135 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 526 HIS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 101 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 50.0000 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN B 129 GLN C 51 GLN C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12071 Z= 0.150 Angle : 0.526 7.806 16838 Z= 0.264 Chirality : 0.040 0.241 2000 Planarity : 0.004 0.044 1872 Dihedral : 17.536 179.152 2881 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 6.32 % Allowed : 28.45 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.15 (0.23), residues: 1346 helix: 1.67 (0.25), residues: 450 sheet: -0.05 (0.30), residues: 282 loop : -1.02 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS D 43 PHE 0.010 0.001 PHE A 391 TYR 0.012 0.001 TYR A 309 ARG 0.005 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 87 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6667 (t80) cc_final: 0.6422 (t80) REVERT: A 90 LYS cc_start: 0.4708 (OUTLIER) cc_final: 0.3602 (mmtp) REVERT: A 95 ASN cc_start: 0.1651 (OUTLIER) cc_final: 0.1302 (m-40) REVERT: A 115 MET cc_start: 0.5112 (mtp) cc_final: 0.4643 (ptp) REVERT: A 295 GLU cc_start: 0.4240 (OUTLIER) cc_final: 0.3700 (tp30) REVERT: A 401 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: A 435 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6982 (pp20) REVERT: A 438 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: B 38 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6505 (ptm160) REVERT: B 123 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6073 (mmpt) REVERT: B 223 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8627 (mt) REVERT: C 90 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: C 504 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7909 (mt) outliers start: 54 outliers final: 29 residues processed: 136 average time/residue: 1.2304 time to fit residues: 182.0460 Evaluate side-chains 125 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 282 ASN C 64 GLN C 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12071 Z= 0.280 Angle : 0.608 11.150 16838 Z= 0.302 Chirality : 0.043 0.362 2000 Planarity : 0.004 0.045 1872 Dihedral : 17.571 178.466 2877 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 7.03 % Allowed : 28.34 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.15 (0.23), residues: 1346 helix: 1.55 (0.25), residues: 450 sheet: 0.07 (0.30), residues: 286 loop : -0.98 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS C 160 PHE 0.031 0.002 PHE C 518 TYR 0.018 0.002 TYR C 513 ARG 0.006 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 86 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.4566 (OUTLIER) cc_final: 0.3447 (mmtp) REVERT: A 95 ASN cc_start: 0.1771 (OUTLIER) cc_final: 0.1356 (m-40) REVERT: A 115 MET cc_start: 0.5087 (mtp) cc_final: 0.4273 (ptt) REVERT: A 401 TRP cc_start: 0.7041 (OUTLIER) cc_final: 0.6115 (m-10) REVERT: A 435 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: B 38 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6878 (ptm160) REVERT: B 123 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6138 (mmpt) REVERT: B 223 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8666 (mt) REVERT: C 504 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7888 (mt) outliers start: 60 outliers final: 40 residues processed: 138 average time/residue: 1.1857 time to fit residues: 178.6744 Evaluate side-chains 133 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 30.0000 chunk 120 optimal weight: 20.0000 chunk 128 optimal weight: 50.0000 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 40.0000 chunk 121 optimal weight: 50.0000 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12071 Z= 0.406 Angle : 0.691 11.018 16838 Z= 0.344 Chirality : 0.046 0.312 2000 Planarity : 0.005 0.045 1872 Dihedral : 17.767 176.984 2877 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 7.73 % Allowed : 27.75 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.08 (0.23), residues: 1346 helix: 1.24 (0.25), residues: 455 sheet: -0.05 (0.30), residues: 286 loop : -1.03 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.005 0.001 HIS C 160 PHE 0.027 0.002 PHE A 294 TYR 0.022 0.002 TYR C 513 ARG 0.006 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 84 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.2033 (OUTLIER) cc_final: 0.1598 (m-40) REVERT: A 115 MET cc_start: 0.5125 (mtp) cc_final: 0.4305 (ptt) REVERT: A 295 GLU cc_start: 0.4390 (OUTLIER) cc_final: 0.3364 (tm-30) REVERT: A 296 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: A 401 TRP cc_start: 0.7124 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: B 38 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7166 (ptm160) REVERT: B 123 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6066 (mmpt) REVERT: B 223 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 504 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7893 (mt) outliers start: 66 outliers final: 39 residues processed: 144 average time/residue: 1.1500 time to fit residues: 180.9342 Evaluate side-chains 130 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 142 optimal weight: 0.0270 chunk 131 optimal weight: 40.0000 chunk 113 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12071 Z= 0.272 Angle : 0.614 11.544 16838 Z= 0.306 Chirality : 0.043 0.310 2000 Planarity : 0.004 0.045 1872 Dihedral : 17.680 178.417 2877 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 6.21 % Allowed : 29.16 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.05 (0.23), residues: 1346 helix: 1.40 (0.25), residues: 451 sheet: 0.02 (0.30), residues: 286 loop : -0.99 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS C 160 PHE 0.025 0.002 PHE C 518 TYR 0.017 0.002 TYR C 513 ARG 0.006 0.000 ARG B 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 86 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6671 (t80) cc_final: 0.6389 (t80) REVERT: A 95 ASN cc_start: 0.2296 (OUTLIER) cc_final: 0.1904 (m-40) REVERT: A 115 MET cc_start: 0.5110 (mtp) cc_final: 0.4297 (ptt) REVERT: A 295 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.3836 (tm-30) REVERT: A 296 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: A 401 TRP cc_start: 0.7045 (OUTLIER) cc_final: 0.6098 (m-10) REVERT: A 435 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6967 (pp20) REVERT: B 38 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6908 (ptm160) REVERT: B 123 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6146 (mmpt) REVERT: B 223 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8631 (mt) REVERT: C 504 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7881 (mt) REVERT: D 49 MET cc_start: 0.6816 (tpp) cc_final: 0.6319 (mmt) outliers start: 53 outliers final: 39 residues processed: 136 average time/residue: 1.1370 time to fit residues: 169.3255 Evaluate side-chains 134 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 50.0000 chunk 47 optimal weight: 0.5980 chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.234696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.182134 restraints weight = 13883.634| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 1.84 r_work: 0.3785 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12071 Z= 0.159 Angle : 0.547 11.201 16838 Z= 0.272 Chirality : 0.041 0.313 2000 Planarity : 0.004 0.043 1872 Dihedral : 17.458 179.158 2877 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 5.39 % Allowed : 29.74 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.23), residues: 1346 helix: 1.79 (0.25), residues: 445 sheet: 0.22 (0.30), residues: 288 loop : -0.82 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 160 PHE 0.018 0.001 PHE A 294 TYR 0.012 0.001 TYR A 369 ARG 0.007 0.000 ARG B 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.29 seconds wall clock time: 69 minutes 2.06 seconds (4142.06 seconds total)