Starting phenix.real_space_refine on Thu Nov 14 12:43:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/11_2024/8gdz_29951.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4079 2.51 5 N 1102 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6320 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1644 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2308 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 170 Chain: "G" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 336 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2017 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.34, per 1000 atoms: 0.69 Number of scatterers: 6320 At special positions: 0 Unit cell: (68.9, 97.52, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1102 8.00 N 1102 7.00 C 4079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 49.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 4.412A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.541A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.507A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.587A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.560A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.637A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.748A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.535A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.274A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.647A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.503A pdb=" N SER R 161 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 4.037A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU R 187 " --> pdb=" O ASN R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 238 removed outlier: 5.059A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.930A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.791A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.002A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.238A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 4.078A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.455A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.678A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.728A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.858A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.556A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2051 1.34 - 1.46: 1604 1.46 - 1.58: 2753 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6458 Sorted by residual: bond pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.26e-02 6.30e+03 2.51e+01 bond pdb=" CA ARG A 232 " pdb=" C ARG A 232 " ideal model delta sigma weight residual 1.521 1.463 0.058 1.17e-02 7.31e+03 2.50e+01 bond pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 1.458 1.415 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 6453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 8784 2.11 - 4.23: 57 4.23 - 6.34: 12 6.34 - 8.46: 2 8.46 - 10.57: 1 Bond angle restraints: 8856 Sorted by residual: angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 110.23 99.66 10.57 1.45e+00 4.76e-01 5.32e+01 angle pdb=" C ARG A 232 " pdb=" N LYS A 233 " pdb=" CA LYS A 233 " ideal model delta sigma weight residual 122.54 116.22 6.32 1.65e+00 3.67e-01 1.47e+01 angle pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 123.00 117.91 5.09 1.41e+00 5.03e-01 1.30e+01 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 124.07 -7.77 3.50e+00 8.16e-02 4.93e+00 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" C GLU B 226 " ideal model delta sigma weight residual 113.88 111.24 2.64 1.23e+00 6.61e-01 4.59e+00 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3425 17.69 - 35.37: 224 35.37 - 53.06: 39 53.06 - 70.75: 8 70.75 - 88.43: 4 Dihedral angle restraints: 3700 sinusoidal: 1063 harmonic: 2637 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 2.43 -88.43 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" C ARG A 231 " pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" CB ARG A 231 " ideal model delta harmonic sigma weight residual -122.60 -114.16 -8.44 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 385 " pdb=" CD ARG A 385 " pdb=" NE ARG A 385 " pdb=" CZ ARG A 385 " ideal model delta sinusoidal sigma weight residual -180.00 -136.01 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 692 0.032 - 0.063: 264 0.063 - 0.095: 80 0.095 - 0.126: 33 0.126 - 0.158: 3 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1069 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO G 49 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 236 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ILE R 205 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.008 2.00e-02 2.50e+03 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1633 2.80 - 3.32: 6136 3.32 - 3.85: 10506 3.85 - 4.37: 11298 4.37 - 4.90: 20569 Nonbonded interactions: 50142 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.280 3.040 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.285 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.351 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.363 3.120 ... (remaining 50137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.003 0.063 6458 Z= 0.232 Angle : 0.509 10.574 8856 Z= 0.277 Chirality : 0.039 0.158 1072 Planarity : 0.003 0.044 1121 Dihedral : 12.959 86.708 1980 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 1.42 (0.28), residues: 886 helix: 2.52 (0.27), residues: 381 sheet: -0.14 (0.38), residues: 175 loop : -0.29 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS R 93 PHE 0.011 0.001 PHE A 222 TYR 0.016 0.001 TYR B 59 ARG 0.006 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.722 Fit side-chains REVERT: B 249 THR cc_start: 0.9229 (p) cc_final: 0.8761 (p) REVERT: B 297 TRP cc_start: 0.8742 (m100) cc_final: 0.8335 (m100) REVERT: R 203 SER cc_start: 0.9392 (t) cc_final: 0.9164 (t) REVERT: R 227 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8402 (mtpt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1564 time to fit residues: 25.0033 Evaluate side-chains 94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 225 HIS B 259 GLN B 340 ASN R 93 HIS R 312 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6458 Z= 0.161 Angle : 0.474 6.456 8856 Z= 0.256 Chirality : 0.040 0.144 1072 Planarity : 0.003 0.042 1121 Dihedral : 3.907 16.205 969 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.93 % Allowed : 9.86 % Favored : 88.20 % 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: 1.50 (0.28), residues: 886 helix: 2.53 (0.27), residues: 391 sheet: -0.04 (0.38), residues: 164 loop : -0.30 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE A 222 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 57 LYS cc_start: 0.9005 (pttp) cc_final: 0.8715 (pttp) REVERT: R 122 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8493 (mm-30) REVERT: R 227 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8396 (mtpt) outliers start: 10 outliers final: 4 residues processed: 106 average time/residue: 0.1429 time to fit residues: 21.5033 Evaluate side-chains 91 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 259 GLN B 340 ASN R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6458 Z= 0.194 Angle : 0.468 6.112 8856 Z= 0.252 Chirality : 0.040 0.142 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.871 16.811 969 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.74 % Allowed : 14.70 % Favored : 83.56 % 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: 1.51 (0.28), residues: 886 helix: 2.51 (0.27), residues: 392 sheet: -0.02 (0.37), residues: 176 loop : -0.27 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE A 212 TYR 0.012 0.001 TYR R 199 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.737 Fit side-chains REVERT: B 57 LYS cc_start: 0.9087 (pttp) cc_final: 0.8804 (pttp) REVERT: R 58 ILE cc_start: 0.8687 (mm) cc_final: 0.8475 (mm) REVERT: R 227 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8444 (mtpt) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.1507 time to fit residues: 22.2337 Evaluate side-chains 92 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 259 GLN B 340 ASN R 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6458 Z= 0.175 Angle : 0.457 7.326 8856 Z= 0.245 Chirality : 0.039 0.145 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.816 17.267 969 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.71 % Allowed : 17.02 % Favored : 80.27 % 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: 1.53 (0.29), residues: 886 helix: 2.56 (0.27), residues: 392 sheet: -0.01 (0.39), residues: 168 loop : -0.32 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 93 PHE 0.009 0.001 PHE A 212 TYR 0.012 0.001 TYR R 199 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.719 Fit side-chains REVERT: B 57 LYS cc_start: 0.9123 (pttp) cc_final: 0.8864 (pttp) REVERT: R 122 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8491 (mm-30) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1406 time to fit residues: 20.8343 Evaluate side-chains 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6458 Z= 0.172 Angle : 0.448 5.874 8856 Z= 0.242 Chirality : 0.039 0.147 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.786 17.312 969 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.51 % Allowed : 18.18 % Favored : 79.30 % 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: 1.60 (0.29), residues: 886 helix: 2.58 (0.27), residues: 392 sheet: 0.04 (0.38), residues: 176 loop : -0.25 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.669 Fit side-chains REVERT: B 57 LYS cc_start: 0.9152 (pttp) cc_final: 0.8908 (pttp) REVERT: R 122 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8366 (mm-30) REVERT: R 227 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8441 (mtpt) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1428 time to fit residues: 20.9047 Evaluate side-chains 98 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6458 Z= 0.156 Angle : 0.444 7.697 8856 Z= 0.238 Chirality : 0.039 0.148 1072 Planarity : 0.003 0.042 1121 Dihedral : 3.746 16.918 969 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.32 % Allowed : 20.31 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 886 helix: 2.57 (0.27), residues: 393 sheet: 0.06 (0.38), residues: 176 loop : -0.24 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE R 104 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.688 Fit side-chains REVERT: B 57 LYS cc_start: 0.9154 (pttp) cc_final: 0.8917 (pttp) REVERT: R 122 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8362 (mm-30) REVERT: R 227 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8439 (mtpt) outliers start: 12 outliers final: 10 residues processed: 114 average time/residue: 0.1439 time to fit residues: 23.3573 Evaluate side-chains 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6458 Z= 0.261 Angle : 0.489 7.174 8856 Z= 0.262 Chirality : 0.040 0.145 1072 Planarity : 0.003 0.042 1121 Dihedral : 3.902 17.415 969 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.90 % Allowed : 21.08 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 886 helix: 2.47 (0.27), residues: 393 sheet: -0.11 (0.37), residues: 181 loop : -0.17 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 178 PHE 0.010 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.798 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.1458 time to fit residues: 21.4921 Evaluate side-chains 96 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 362 HIS B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6458 Z= 0.154 Angle : 0.457 7.426 8856 Z= 0.245 Chirality : 0.039 0.149 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.786 17.357 969 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.71 % Allowed : 21.28 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 886 helix: 2.55 (0.27), residues: 393 sheet: -0.04 (0.38), residues: 176 loop : -0.22 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE R 289 TYR 0.021 0.001 TYR R 185 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.752 Fit side-chains REVERT: R 122 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8498 (mm-30) REVERT: R 227 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8448 (mtpt) outliers start: 14 outliers final: 11 residues processed: 105 average time/residue: 0.1435 time to fit residues: 21.5927 Evaluate side-chains 100 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6458 Z= 0.186 Angle : 0.477 8.121 8856 Z= 0.254 Chirality : 0.040 0.146 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.776 17.303 969 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.71 % Allowed : 21.28 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 886 helix: 2.54 (0.27), residues: 393 sheet: -0.07 (0.38), residues: 176 loop : -0.22 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 178 PHE 0.009 0.001 PHE A 212 TYR 0.020 0.001 TYR R 185 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.711 Fit side-chains REVERT: B 273 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8253 (mp) REVERT: R 122 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8483 (mm-30) REVERT: R 227 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8443 (mtpt) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.1333 time to fit residues: 19.5389 Evaluate side-chains 101 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 56 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6458 Z= 0.145 Angle : 0.464 7.718 8856 Z= 0.247 Chirality : 0.039 0.146 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.706 17.054 969 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.51 % Allowed : 21.86 % Favored : 75.63 % 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: 1.56 (0.29), residues: 886 helix: 2.60 (0.27), residues: 392 sheet: -0.12 (0.38), residues: 178 loop : -0.24 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 93 PHE 0.010 0.001 PHE R 289 TYR 0.014 0.001 TYR R 185 ARG 0.004 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.683 Fit side-chains REVERT: R 122 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8394 (mm-30) REVERT: R 173 TRP cc_start: 0.8841 (m-10) cc_final: 0.8537 (m-10) REVERT: R 227 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8436 (mtpt) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.1462 time to fit residues: 22.3237 Evaluate side-chains 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 225 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095934 restraints weight = 12957.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098811 restraints weight = 6112.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100716 restraints weight = 3712.490| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6458 Z= 0.174 Angle : 0.465 7.497 8856 Z= 0.248 Chirality : 0.040 0.145 1072 Planarity : 0.003 0.041 1121 Dihedral : 3.714 17.326 969 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.51 % Allowed : 21.86 % Favored : 75.63 % 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: 1.53 (0.29), residues: 886 helix: 2.61 (0.27), residues: 390 sheet: -0.15 (0.39), residues: 173 loop : -0.27 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 178 PHE 0.009 0.001 PHE A 212 TYR 0.013 0.001 TYR R 185 ARG 0.004 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.79 seconds wall clock time: 39 minutes 19.83 seconds (2359.83 seconds total)