Starting phenix.real_space_refine on Sun Nov 17 01:42:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t0q_40945/11_2024/8t0q_40945_trim.cif" } resolution = 3.06 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= 0.003 sd= 0.050 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 Co 2 6.85 5 P 4 5.49 5 S 64 5.16 5 C 7879 2.51 5 N 2082 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12355 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1992 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1983 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "C" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4066 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "D" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4066 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 18, 'TRANS': 498} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'B12': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Unsupported chir.volume_sign: {'cros': 1} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'B12': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Unsupported chir.volume_sign: {'cros': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'5AD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'5AD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.58, per 1000 atoms: 0.61 Number of scatterers: 12355 At special positions: 0 Unit cell: (99.076, 89.59, 154.938, 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) Co 2 26.99 S 64 16.00 P 4 15.00 O 2324 8.00 N 2082 7.00 C 7879 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2846 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 55.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 45 through 59 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.885A pdb=" N ILE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 263 through 267 removed outlier: 4.087A pdb=" N GLY A 266 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.624A pdb=" N THR B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 244 through 259 removed outlier: 3.618A pdb=" N VAL B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.807A pdb=" N GLY B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 33 removed outlier: 3.653A pdb=" N LYS C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 89 removed outlier: 4.216A pdb=" N THR C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 113 through 147 removed outlier: 3.665A pdb=" N LEU C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 removed outlier: 4.394A pdb=" N VAL C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 removed outlier: 3.540A pdb=" N LEU C 191 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 229 Processing helix chain 'C' and resid 242 through 253 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 272 through 291 removed outlier: 3.638A pdb=" N PHE C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 4.135A pdb=" N LEU C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 328 removed outlier: 6.072A pdb=" N HIS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N THR C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 349 through 365 Processing helix chain 'C' and resid 382 through 401 Processing helix chain 'C' and resid 418 through 436 Processing helix chain 'C' and resid 449 through 473 Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 508 through 516 removed outlier: 4.123A pdb=" N ASP C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 32 removed outlier: 3.551A pdb=" N LYS D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.533A pdb=" N ARG D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.564A pdb=" N TYR D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 113 through 147 removed outlier: 4.017A pdb=" N ILE D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 177 removed outlier: 4.063A pdb=" N VAL D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 210 through 229 Processing helix chain 'D' and resid 242 through 253 Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.590A pdb=" N ARG D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 291 removed outlier: 3.786A pdb=" N PHE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 4.192A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 328 removed outlier: 3.684A pdb=" N VAL D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 349 through 365 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.507A pdb=" N VAL D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 436 Processing helix chain 'D' and resid 438 through 442 removed outlier: 3.515A pdb=" N GLU D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 442' Processing helix chain 'D' and resid 449 through 473 Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.793A pdb=" N GLU D 479 " --> pdb=" O PHE D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 508 through 516 removed outlier: 3.827A pdb=" N ASP D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 73 removed outlier: 5.562A pdb=" N VAL A 66 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 82 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 68 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 72 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 83 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS A 33 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR B 39 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR B 82 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL B 66 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 6.349A pdb=" N VAL A 121 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TYR A 161 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 123 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 122 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 185 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 124 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER A 187 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA A 126 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.426A pdb=" N VAL B 121 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR B 161 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 123 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 122 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 185 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 124 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.309A pdb=" N ILE C 294 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 234 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU C 259 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN C 236 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 181 " --> pdb=" O CYS C 235 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR C 237 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL C 183 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 154 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA C 182 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 156 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU C 153 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR C 372 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AA8, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.195A pdb=" N ILE D 294 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU D 234 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU D 259 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN D 236 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 181 " --> pdb=" O CYS D 235 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N TYR D 237 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N VAL D 183 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 153 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N HIS D 339 " --> pdb=" O MET D 373 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 2118 1.29 - 1.44: 3093 1.44 - 1.59: 7248 1.59 - 1.74: 2 1.74 - 1.89: 128 Bond restraints: 12589 Sorted by residual: bond pdb=" C4 B12 A 401 " pdb=" N21 B12 A 401 " ideal model delta sigma weight residual 1.416 1.207 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C14 B12 A 401 " pdb=" N23 B12 A 401 " ideal model delta sigma weight residual 1.416 1.242 0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C4 B12 B 401 " pdb=" N21 B12 B 401 " ideal model delta sigma weight residual 1.416 1.244 0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" C19 B12 B 401 " pdb=" N24 B12 B 401 " ideal model delta sigma weight residual 1.416 1.582 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C14 B12 B 401 " pdb=" N23 B12 B 401 " ideal model delta sigma weight residual 1.416 1.256 0.160 2.00e-02 2.50e+03 6.43e+01 ... (remaining 12584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 16897 4.53 - 9.06: 122 9.06 - 13.59: 30 13.59 - 18.12: 12 18.12 - 22.65: 7 Bond angle restraints: 17068 Sorted by residual: angle pdb=" N GLY B 222 " pdb=" CA GLY B 222 " pdb=" C GLY B 222 " ideal model delta sigma weight residual 112.34 134.99 -22.65 2.04e+00 2.40e-01 1.23e+02 angle pdb=" C4 B12 B 401 " pdb=" N21 B12 B 401 " pdb="CO B12 B 401 " ideal model delta sigma weight residual 109.50 130.79 -21.29 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C19 B12 A 401 " pdb=" C18 B12 A 401 " pdb=" C60 B12 A 401 " ideal model delta sigma weight residual 109.47 89.48 19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" C16 B12 B 401 " pdb=" C17 B12 B 401 " pdb=" C55 B12 B 401 " ideal model delta sigma weight residual 109.47 128.38 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C4 B12 A 401 " pdb=" N21 B12 A 401 " pdb="CO B12 A 401 " ideal model delta sigma weight residual 109.50 128.29 -18.79 3.00e+00 1.11e-01 3.92e+01 ... (remaining 17063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 7299 34.75 - 69.50: 283 69.50 - 104.24: 27 104.24 - 138.99: 3 138.99 - 173.74: 4 Dihedral angle restraints: 7616 sinusoidal: 3163 harmonic: 4453 Sorted by residual: dihedral pdb=" C5A PLP A 402 " pdb=" O4P PLP A 402 " pdb=" P PLP A 402 " pdb=" O1P PLP A 402 " ideal model delta sinusoidal sigma weight residual 76.43 -97.31 173.74 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3R B12 B 401 " pdb=" O2 B12 B 401 " pdb=" P B12 B 401 " pdb=" O4 B12 B 401 " ideal model delta sinusoidal sigma weight residual 60.00 -130.12 -169.87 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C3R B12 A 401 " pdb=" O2 B12 A 401 " pdb=" P B12 A 401 " pdb=" O4 B12 A 401 " ideal model delta sinusoidal sigma weight residual 60.00 -139.71 -160.29 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 7613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.101: 1921 1.101 - 2.201: 0 2.201 - 3.302: 4 3.302 - 4.402: 0 4.402 - 5.503: 4 Chirality restraints: 1929 Sorted by residual: chirality pdb=" N24 B12 B 401 " pdb=" C16 B12 B 401 " pdb=" C19 B12 B 401 " pdb="CO B12 B 401 " both_signs ideal model delta sigma weight residual False -2.93 2.57 -5.50 2.00e-01 2.50e+01 7.57e+02 chirality pdb=" C12 B12 A 401 " pdb=" C11 B12 A 401 " pdb=" C46 B12 A 401 " pdb=" C47 B12 A 401 " both_signs ideal model delta sigma weight residual False -2.64 2.53 -5.17 2.00e-01 2.50e+01 6.68e+02 chirality pdb=" C12 B12 B 401 " pdb=" C11 B12 B 401 " pdb=" C46 B12 B 401 " pdb=" C47 B12 B 401 " both_signs ideal model delta sigma weight residual False -2.64 2.45 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 1926 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 B12 A 401 " 0.132 2.00e-02 2.50e+03 2.08e-01 4.32e+02 pdb=" C18 B12 A 401 " 0.128 2.00e-02 2.50e+03 pdb=" C19 B12 A 401 " -0.359 2.00e-02 2.50e+03 pdb=" N24 B12 A 401 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 B12 A 401 " 0.181 2.00e-02 2.50e+03 1.64e-01 4.04e+02 pdb=" C15 B12 A 401 " 0.036 2.00e-02 2.50e+03 pdb=" C16 B12 A 401 " 0.023 2.00e-02 2.50e+03 pdb=" C17 B12 A 401 " 0.188 2.00e-02 2.50e+03 pdb=" C53 B12 A 401 " -0.202 2.00e-02 2.50e+03 pdb=" N24 B12 A 401 " -0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C35 B12 A 401 " 0.187 2.00e-02 2.50e+03 1.48e-01 3.30e+02 pdb=" C4 B12 A 401 " -0.165 2.00e-02 2.50e+03 pdb=" C5 B12 A 401 " -0.023 2.00e-02 2.50e+03 pdb=" C6 B12 A 401 " -0.030 2.00e-02 2.50e+03 pdb=" C7 B12 A 401 " -0.169 2.00e-02 2.50e+03 pdb=" N22 B12 A 401 " 0.200 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 64 2.37 - 3.00: 7587 3.00 - 3.63: 18701 3.63 - 4.27: 28694 4.27 - 4.90: 48334 Nonbonded interactions: 103380 Sorted by model distance: nonbonded pdb=" OG SER D 190 " pdb=" O1P PLP B 402 " model vdw 1.734 3.040 nonbonded pdb=" OH TYR C 146 " pdb=" OE1 GLU C 226 " model vdw 1.966 3.040 nonbonded pdb=" OH TYR D 146 " pdb=" OE1 GLU D 226 " model vdw 1.990 3.040 nonbonded pdb=" OG1 THR C 296 " pdb=" OE1 GLU C 298 " model vdw 2.005 3.040 nonbonded pdb=" OD1 ASP A 73 " pdb=" N LYS A 74 " model vdw 2.032 3.120 ... (remaining 103375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 268 or resid 401 through 402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.750 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.900 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.008 0.209 12589 Z= 0.541 Angle : 1.064 22.646 17068 Z= 0.424 Chirality : 0.275 5.503 1929 Planarity : 0.008 0.208 2186 Dihedral : 18.271 173.739 4770 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 38.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.90 % Favored : 95.78 % Rotamer: Outliers : 3.74 % Allowed : 27.59 % Favored : 68.67 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1539 helix: 2.15 (0.19), residues: 788 sheet: -1.20 (0.37), residues: 212 loop : 0.44 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 10 HIS 0.008 0.001 HIS A 133 PHE 0.016 0.001 PHE C 341 TYR 0.018 0.001 TYR B 146 ARG 0.022 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: C 270 ASP cc_start: 0.8022 (t0) cc_final: 0.7645 (t0) outliers start: 48 outliers final: 44 residues processed: 291 average time/residue: 0.2409 time to fit residues: 101.6152 Evaluate side-chains 290 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 235 CYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 387 HIS Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 511 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 247 HIS C 176 GLN ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12589 Z= 0.362 Angle : 1.021 31.820 17068 Z= 0.423 Chirality : 0.100 2.570 1929 Planarity : 0.005 0.048 2186 Dihedral : 13.046 142.795 1891 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 5.07 % Allowed : 21.51 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1539 helix: 2.03 (0.18), residues: 777 sheet: -1.16 (0.36), residues: 209 loop : 0.29 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 10 HIS 0.004 0.001 HIS D 415 PHE 0.021 0.002 PHE C 341 TYR 0.022 0.002 TYR C 444 ARG 0.007 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 1.507 Fit side-chains REVERT: A 28 THR cc_start: 0.8807 (t) cc_final: 0.8565 (p) REVERT: B 104 MET cc_start: 0.7782 (tmt) cc_final: 0.6851 (tmt) REVERT: B 106 MET cc_start: 0.7708 (tpt) cc_final: 0.6850 (tpt) REVERT: B 108 GLU cc_start: 0.8095 (mp0) cc_final: 0.7892 (pm20) REVERT: B 112 TYR cc_start: 0.7608 (t80) cc_final: 0.7262 (t80) REVERT: B 141 MET cc_start: 0.6381 (mtp) cc_final: 0.6011 (mtp) REVERT: C 165 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7901 (tm-30) REVERT: C 169 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8380 (mm110) REVERT: C 243 MET cc_start: 0.8820 (mtm) cc_final: 0.8533 (ttp) REVERT: C 270 ASP cc_start: 0.8291 (t0) cc_final: 0.7769 (t0) REVERT: C 301 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: C 335 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: C 373 MET cc_start: 0.9000 (mtp) cc_final: 0.8780 (mtp) REVERT: C 427 GLU cc_start: 0.8052 (tp30) cc_final: 0.7813 (tp30) REVERT: C 442 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7741 (mt-10) REVERT: D 98 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8541 (mtt180) REVERT: D 140 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7982 (tm-30) REVERT: D 189 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: D 256 ASP cc_start: 0.8626 (m-30) cc_final: 0.8423 (m-30) REVERT: D 442 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7824 (mm-30) outliers start: 65 outliers final: 34 residues processed: 308 average time/residue: 0.2520 time to fit residues: 110.9877 Evaluate side-chains 280 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 63 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 199 ASN ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12589 Z= 0.262 Angle : 0.955 31.641 17068 Z= 0.388 Chirality : 0.095 2.535 1929 Planarity : 0.004 0.050 2186 Dihedral : 11.323 136.325 1836 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 4.60 % Allowed : 21.12 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1539 helix: 2.05 (0.19), residues: 778 sheet: -1.26 (0.35), residues: 210 loop : 0.30 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.022 0.001 PHE D 341 TYR 0.018 0.001 TYR C 444 ARG 0.009 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 1.497 Fit side-chains REVERT: A 28 THR cc_start: 0.8797 (t) cc_final: 0.8573 (p) REVERT: B 104 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6773 (tmt) REVERT: B 106 MET cc_start: 0.7723 (tpt) cc_final: 0.7238 (tpt) REVERT: B 112 TYR cc_start: 0.7450 (t80) cc_final: 0.7209 (t80) REVERT: B 141 MET cc_start: 0.6570 (mtp) cc_final: 0.6298 (mtp) REVERT: C 12 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8172 (tm) REVERT: C 98 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7513 (mtt180) REVERT: C 217 MET cc_start: 0.8824 (tpp) cc_final: 0.8603 (tpt) REVERT: C 243 MET cc_start: 0.8780 (mtm) cc_final: 0.8474 (ttp) REVERT: C 270 ASP cc_start: 0.8310 (t0) cc_final: 0.7830 (t0) REVERT: C 273 MET cc_start: 0.8647 (ptp) cc_final: 0.8354 (ptm) REVERT: C 373 MET cc_start: 0.8983 (mtp) cc_final: 0.8759 (mtp) REVERT: C 442 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7786 (mt-10) REVERT: C 472 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7280 (mp0) REVERT: D 41 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: D 98 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8598 (mtt180) REVERT: D 140 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8082 (tm-30) REVERT: D 189 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: D 256 ASP cc_start: 0.8586 (m-30) cc_final: 0.8381 (m-30) REVERT: D 343 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8643 (mtp) REVERT: D 412 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 476 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7919 (mmmt) outliers start: 59 outliers final: 28 residues processed: 289 average time/residue: 0.2557 time to fit residues: 105.7147 Evaluate side-chains 282 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 142 ASN C 169 GLN ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12589 Z= 0.316 Angle : 0.958 31.699 17068 Z= 0.394 Chirality : 0.095 2.512 1929 Planarity : 0.004 0.054 2186 Dihedral : 11.019 132.273 1828 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 4.91 % Allowed : 20.34 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1539 helix: 1.91 (0.19), residues: 779 sheet: -1.32 (0.35), residues: 210 loop : 0.19 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 10 HIS 0.005 0.001 HIS C 339 PHE 0.019 0.002 PHE C 341 TYR 0.018 0.001 TYR D 155 ARG 0.010 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 1.443 Fit side-chains REVERT: A 28 THR cc_start: 0.8831 (t) cc_final: 0.8583 (p) REVERT: B 104 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6856 (tmt) REVERT: B 106 MET cc_start: 0.7738 (tpt) cc_final: 0.7215 (tpt) REVERT: B 141 MET cc_start: 0.6659 (mtp) cc_final: 0.6294 (mtp) REVERT: C 12 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8189 (tm) REVERT: C 98 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7518 (mtt180) REVERT: C 217 MET cc_start: 0.8831 (tpp) cc_final: 0.8598 (tpt) REVERT: C 243 MET cc_start: 0.8759 (mtm) cc_final: 0.8444 (ttp) REVERT: C 270 ASP cc_start: 0.8370 (t0) cc_final: 0.7883 (t0) REVERT: C 273 MET cc_start: 0.8675 (ptp) cc_final: 0.8384 (ptm) REVERT: C 335 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: C 373 MET cc_start: 0.9010 (mtp) cc_final: 0.8727 (mtp) REVERT: C 472 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7245 (mp0) REVERT: D 41 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: D 98 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8572 (mtt180) REVERT: D 101 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8639 (mtpm) REVERT: D 103 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7957 (mp0) REVERT: D 140 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 165 GLU cc_start: 0.8368 (mp0) cc_final: 0.8054 (mp0) REVERT: D 189 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: D 261 ASP cc_start: 0.8439 (t0) cc_final: 0.8110 (m-30) REVERT: D 280 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7858 (pp30) REVERT: D 343 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: D 379 MET cc_start: 0.9144 (mmt) cc_final: 0.8857 (mmp) REVERT: D 442 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7735 (mm-30) REVERT: D 476 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7935 (mmmt) outliers start: 63 outliers final: 42 residues processed: 295 average time/residue: 0.2508 time to fit residues: 106.0433 Evaluate side-chains 290 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.0010 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 142 ASN B 169 ASN C 387 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12589 Z= 0.325 Angle : 0.958 31.725 17068 Z= 0.395 Chirality : 0.094 2.507 1929 Planarity : 0.004 0.052 2186 Dihedral : 10.932 129.319 1828 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 4.99 % Allowed : 19.72 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1539 helix: 1.89 (0.19), residues: 779 sheet: -1.34 (0.35), residues: 209 loop : 0.13 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 10 HIS 0.005 0.001 HIS C 339 PHE 0.020 0.002 PHE C 341 TYR 0.017 0.001 TYR D 155 ARG 0.011 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 1.353 Fit side-chains REVERT: A 28 THR cc_start: 0.8841 (t) cc_final: 0.8527 (p) REVERT: A 134 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7629 (p) REVERT: B 18 ASP cc_start: 0.8356 (t0) cc_final: 0.7921 (t0) REVERT: B 104 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7001 (tmt) REVERT: B 106 MET cc_start: 0.7748 (tpt) cc_final: 0.6816 (tpp) REVERT: B 112 TYR cc_start: 0.7590 (t80) cc_final: 0.7384 (t80) REVERT: B 141 MET cc_start: 0.6725 (mtp) cc_final: 0.6342 (mtp) REVERT: B 187 SER cc_start: 0.7269 (t) cc_final: 0.6218 (p) REVERT: C 12 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8214 (tm) REVERT: C 98 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7531 (mtt180) REVERT: C 217 MET cc_start: 0.8837 (tpp) cc_final: 0.8583 (tpt) REVERT: C 243 MET cc_start: 0.8769 (mtm) cc_final: 0.8468 (ttp) REVERT: C 270 ASP cc_start: 0.8245 (t0) cc_final: 0.7830 (t0) REVERT: C 301 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: C 335 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8495 (mtp) REVERT: C 373 MET cc_start: 0.9007 (mtp) cc_final: 0.8690 (mtp) REVERT: C 472 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7285 (mp0) REVERT: D 98 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8579 (mtt180) REVERT: D 101 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8651 (mtpm) REVERT: D 103 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7976 (mp0) REVERT: D 140 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 165 GLU cc_start: 0.8378 (mp0) cc_final: 0.8062 (mp0) REVERT: D 169 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8432 (mm-40) REVERT: D 189 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: D 280 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7860 (pp30) REVERT: D 390 ASP cc_start: 0.8538 (m-30) cc_final: 0.8139 (m-30) REVERT: D 442 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7814 (mm-30) REVERT: D 476 LYS cc_start: 0.8362 (mmtp) cc_final: 0.7963 (mmmt) outliers start: 64 outliers final: 44 residues processed: 287 average time/residue: 0.2420 time to fit residues: 99.8855 Evaluate side-chains 299 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 343 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.3980 chunk 132 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12589 Z= 0.205 Angle : 0.933 31.799 17068 Z= 0.381 Chirality : 0.092 2.506 1929 Planarity : 0.004 0.050 2186 Dihedral : 10.502 129.917 1826 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer: Outliers : 3.82 % Allowed : 21.90 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1539 helix: 2.06 (0.19), residues: 778 sheet: -1.30 (0.36), residues: 210 loop : 0.22 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.018 0.001 PHE D 341 TYR 0.017 0.001 TYR D 197 ARG 0.012 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.298 Fit side-chains REVERT: A 28 THR cc_start: 0.8871 (t) cc_final: 0.8551 (p) REVERT: A 84 SER cc_start: 0.8923 (m) cc_final: 0.8619 (p) REVERT: A 134 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7743 (p) REVERT: A 210 GLU cc_start: 0.8744 (tp30) cc_final: 0.8274 (tp30) REVERT: B 18 ASP cc_start: 0.8277 (t0) cc_final: 0.7808 (t0) REVERT: B 50 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 104 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.6851 (tmm) REVERT: B 106 MET cc_start: 0.7619 (tpt) cc_final: 0.6683 (tpp) REVERT: B 112 TYR cc_start: 0.7530 (t80) cc_final: 0.7293 (t80) REVERT: B 141 MET cc_start: 0.6824 (mtp) cc_final: 0.6452 (mtp) REVERT: B 187 SER cc_start: 0.7241 (t) cc_final: 0.6140 (p) REVERT: C 98 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: C 217 MET cc_start: 0.8822 (tpp) cc_final: 0.8568 (tpt) REVERT: C 243 MET cc_start: 0.8710 (mtm) cc_final: 0.8389 (ttp) REVERT: C 270 ASP cc_start: 0.8190 (t0) cc_final: 0.7830 (t0) REVERT: C 335 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: C 373 MET cc_start: 0.8978 (mtp) cc_final: 0.8677 (mtp) REVERT: C 472 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7374 (mp0) REVERT: D 41 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7688 (mtm-85) REVERT: D 80 TYR cc_start: 0.8728 (m-80) cc_final: 0.8171 (m-80) REVERT: D 98 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8649 (mtt180) REVERT: D 101 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8274 (mtpm) REVERT: D 140 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8004 (tm-30) REVERT: D 165 GLU cc_start: 0.8346 (mp0) cc_final: 0.8136 (mp0) REVERT: D 189 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8325 (tt0) REVERT: D 261 ASP cc_start: 0.8433 (t0) cc_final: 0.8152 (m-30) REVERT: D 390 ASP cc_start: 0.8480 (m-30) cc_final: 0.8082 (m-30) REVERT: D 442 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7739 (mm-30) outliers start: 49 outliers final: 30 residues processed: 290 average time/residue: 0.2560 time to fit residues: 105.8719 Evaluate side-chains 281 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 63 ASN B 169 ASN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12589 Z= 0.329 Angle : 0.968 31.474 17068 Z= 0.404 Chirality : 0.094 2.507 1929 Planarity : 0.005 0.053 2186 Dihedral : 10.467 130.511 1825 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 4.52 % Allowed : 21.59 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1539 helix: 1.96 (0.19), residues: 778 sheet: -1.32 (0.36), residues: 209 loop : 0.13 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 10 HIS 0.005 0.001 HIS C 339 PHE 0.021 0.002 PHE C 341 TYR 0.020 0.001 TYR D 197 ARG 0.013 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 1.448 Fit side-chains REVERT: A 84 SER cc_start: 0.8926 (m) cc_final: 0.8638 (p) REVERT: A 134 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7663 (p) REVERT: B 18 ASP cc_start: 0.8368 (t0) cc_final: 0.7882 (t0) REVERT: B 50 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 104 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7208 (tmt) REVERT: B 106 MET cc_start: 0.7726 (tpt) cc_final: 0.7388 (tpt) REVERT: B 141 MET cc_start: 0.6977 (mtp) cc_final: 0.6603 (mtp) REVERT: B 187 SER cc_start: 0.7431 (t) cc_final: 0.6268 (p) REVERT: C 98 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7518 (mtt180) REVERT: C 217 MET cc_start: 0.8839 (tpp) cc_final: 0.8567 (tpt) REVERT: C 243 MET cc_start: 0.8752 (mtm) cc_final: 0.8470 (ttp) REVERT: C 270 ASP cc_start: 0.8262 (t0) cc_final: 0.7837 (t0) REVERT: C 335 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: C 373 MET cc_start: 0.9029 (mtp) cc_final: 0.8686 (mtp) REVERT: C 472 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7282 (mp0) REVERT: D 98 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8526 (mtt180) REVERT: D 101 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8651 (ttpp) REVERT: D 140 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 165 GLU cc_start: 0.8399 (mp0) cc_final: 0.8120 (mp0) REVERT: D 169 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8360 (mm-40) REVERT: D 189 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: D 261 ASP cc_start: 0.8428 (t0) cc_final: 0.8112 (m-30) REVERT: D 390 ASP cc_start: 0.8555 (m-30) cc_final: 0.8120 (m-30) REVERT: D 470 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 476 LYS cc_start: 0.8380 (mmtp) cc_final: 0.7977 (mmmt) outliers start: 58 outliers final: 41 residues processed: 284 average time/residue: 0.2503 time to fit residues: 102.3808 Evaluate side-chains 298 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 HIS B 63 ASN B 169 ASN C 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12589 Z= 0.237 Angle : 0.959 31.591 17068 Z= 0.398 Chirality : 0.093 2.500 1929 Planarity : 0.004 0.051 2186 Dihedral : 10.215 131.728 1825 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 22.21 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1539 helix: 1.99 (0.19), residues: 778 sheet: -1.31 (0.36), residues: 209 loop : 0.10 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.020 0.001 PHE C 341 TYR 0.021 0.001 TYR D 197 ARG 0.014 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.385 Fit side-chains REVERT: A 84 SER cc_start: 0.8911 (m) cc_final: 0.8631 (p) REVERT: A 210 GLU cc_start: 0.8791 (tp30) cc_final: 0.8337 (tp30) REVERT: B 18 ASP cc_start: 0.8329 (t0) cc_final: 0.7828 (t0) REVERT: B 50 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 104 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.6813 (tmm) REVERT: B 106 MET cc_start: 0.7668 (tpt) cc_final: 0.6778 (tpp) REVERT: B 141 MET cc_start: 0.7016 (mtp) cc_final: 0.6680 (mtp) REVERT: B 187 SER cc_start: 0.7457 (t) cc_final: 0.6297 (p) REVERT: C 98 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7525 (mtt180) REVERT: C 217 MET cc_start: 0.8841 (tpp) cc_final: 0.8567 (tpt) REVERT: C 243 MET cc_start: 0.8730 (mtm) cc_final: 0.8480 (ttp) REVERT: C 270 ASP cc_start: 0.8226 (t0) cc_final: 0.7836 (t0) REVERT: C 335 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: C 373 MET cc_start: 0.8998 (mtp) cc_final: 0.8712 (mtp) REVERT: D 98 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8539 (mtt180) REVERT: D 101 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (ttpp) REVERT: D 140 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 189 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: D 261 ASP cc_start: 0.8419 (t0) cc_final: 0.8108 (m-30) REVERT: D 390 ASP cc_start: 0.8524 (m-30) cc_final: 0.8074 (m-30) REVERT: D 442 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7649 (mm-30) REVERT: D 470 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 476 LYS cc_start: 0.8329 (mmtp) cc_final: 0.7929 (mmmt) outliers start: 51 outliers final: 38 residues processed: 288 average time/residue: 0.2606 time to fit residues: 106.8104 Evaluate side-chains 299 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 247 HIS B 63 ASN B 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12589 Z= 0.245 Angle : 0.963 31.489 17068 Z= 0.401 Chirality : 0.092 2.493 1929 Planarity : 0.005 0.055 2186 Dihedral : 10.040 131.046 1825 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 4.13 % Allowed : 22.37 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1539 helix: 1.98 (0.19), residues: 778 sheet: -1.31 (0.36), residues: 209 loop : 0.07 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.020 0.001 PHE C 341 TYR 0.022 0.001 TYR D 197 ARG 0.013 0.001 ARG C 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 1.513 Fit side-chains REVERT: A 84 SER cc_start: 0.8901 (m) cc_final: 0.8624 (p) REVERT: A 210 GLU cc_start: 0.8807 (tp30) cc_final: 0.8357 (tp30) REVERT: B 50 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 104 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.6830 (tmm) REVERT: B 106 MET cc_start: 0.7677 (tpt) cc_final: 0.7338 (tpt) REVERT: B 141 MET cc_start: 0.6978 (mtp) cc_final: 0.6593 (mtp) REVERT: B 187 SER cc_start: 0.7528 (t) cc_final: 0.6361 (p) REVERT: C 98 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: C 217 MET cc_start: 0.8854 (tpp) cc_final: 0.8576 (tpt) REVERT: C 243 MET cc_start: 0.8706 (mtm) cc_final: 0.8416 (ttp) REVERT: C 270 ASP cc_start: 0.8245 (t0) cc_final: 0.7835 (t0) REVERT: C 335 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8441 (mtp) REVERT: C 373 MET cc_start: 0.8999 (mtp) cc_final: 0.8703 (mtp) REVERT: D 98 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8549 (mtt180) REVERT: D 101 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8649 (ttpp) REVERT: D 140 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 189 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: D 261 ASP cc_start: 0.8424 (t0) cc_final: 0.8114 (m-30) REVERT: D 390 ASP cc_start: 0.8526 (m-30) cc_final: 0.8068 (m-30) REVERT: D 442 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 470 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 476 LYS cc_start: 0.8330 (mmtp) cc_final: 0.7923 (mmmt) outliers start: 53 outliers final: 42 residues processed: 277 average time/residue: 0.2604 time to fit residues: 103.1268 Evaluate side-chains 298 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 387 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 100 optimal weight: 0.0170 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 120 optimal weight: 0.0040 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS B 63 ASN B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12589 Z= 0.198 Angle : 0.952 31.455 17068 Z= 0.395 Chirality : 0.091 2.477 1929 Planarity : 0.005 0.058 2186 Dihedral : 9.765 129.568 1823 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 23.38 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1539 helix: 2.08 (0.19), residues: 778 sheet: -1.23 (0.37), residues: 199 loop : 0.08 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.019 0.001 PHE B 172 TYR 0.022 0.001 TYR D 197 ARG 0.017 0.001 ARG C 516 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 1.435 Fit side-chains REVERT: A 84 SER cc_start: 0.8893 (m) cc_final: 0.8609 (p) REVERT: A 210 GLU cc_start: 0.8811 (tp30) cc_final: 0.8363 (tp30) REVERT: B 50 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 63 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8709 (t0) REVERT: B 104 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.6881 (tmm) REVERT: B 106 MET cc_start: 0.7594 (tpt) cc_final: 0.7323 (tpt) REVERT: B 141 MET cc_start: 0.6874 (mtp) cc_final: 0.6529 (mtp) REVERT: B 187 SER cc_start: 0.7574 (t) cc_final: 0.6399 (p) REVERT: C 98 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7498 (mtt180) REVERT: C 217 MET cc_start: 0.8817 (tpp) cc_final: 0.8545 (tpt) REVERT: C 243 MET cc_start: 0.8646 (mtm) cc_final: 0.8401 (ttp) REVERT: C 270 ASP cc_start: 0.8211 (t0) cc_final: 0.7875 (t0) REVERT: C 335 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8315 (mtp) REVERT: D 101 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: D 140 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 189 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8371 (tm-30) REVERT: D 217 MET cc_start: 0.8601 (tpp) cc_final: 0.8250 (mmm) REVERT: D 261 ASP cc_start: 0.8424 (t0) cc_final: 0.8114 (m-30) REVERT: D 442 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 470 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 476 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7861 (mmmt) outliers start: 40 outliers final: 30 residues processed: 283 average time/residue: 0.2591 time to fit residues: 105.2315 Evaluate side-chains 280 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082795 restraints weight = 22033.521| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.32 r_work: 0.3061 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 12589 Z= 0.310 Angle : 1.243 59.200 17068 Z= 0.648 Chirality : 0.096 2.478 1929 Planarity : 0.005 0.101 2186 Dihedral : 9.781 129.541 1821 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.31 % Favored : 96.56 % Rotamer: Outliers : 2.96 % Allowed : 23.62 % Favored : 73.42 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.31 (0.22), residues: 1539 helix: 2.07 (0.19), residues: 778 sheet: -1.24 (0.37), residues: 199 loop : 0.08 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 10 HIS 0.005 0.001 HIS C 339 PHE 0.018 0.001 PHE C 341 TYR 0.020 0.001 TYR D 197 ARG 0.014 0.001 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.09 seconds wall clock time: 54 minutes 41.66 seconds (3281.66 seconds total)