Starting phenix.real_space_refine on Tue Mar 11 20:06:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge3_29954/03_2025/8ge3_29954.cif" } resolution = 3.3 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= 0.035 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 42 5.16 5 C 4263 2.51 5 N 1145 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6606 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1714 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2413 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 111 Chain: "G" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 345 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2119 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 106 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: 4.43, per 1000 atoms: 0.67 Number of scatterers: 6606 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 42 16.00 O 1156 8.00 N 1145 7.00 C 4263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.58 Conformation dependent library (CDL) restraints added in 895.8 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 48.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.573A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.656A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.638A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.761A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.507A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.654A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.592A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.545A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.612A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.683A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.483A 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 137 through 145 removed outlier: 4.237A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.688A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.834A 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 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.803A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.885A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.915A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (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 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 9.444A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.133A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.617A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.419A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.619A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.024A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.139A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1149 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: 1.79 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2133 1.35 - 1.46: 1730 1.46 - 1.58: 2830 1.58 - 1.70: 0 1.70 - 1.82: 59 Bond restraints: 6752 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.566 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.323 0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 9086 1.48 - 2.97: 111 2.97 - 4.45: 19 4.45 - 5.93: 12 5.93 - 7.42: 1 Bond angle restraints: 9229 Sorted by residual: angle pdb=" C ASN A 264 " pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" CB GLU R 180 " pdb=" CG GLU R 180 " pdb=" CD GLU R 180 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.70e+00 3.46e-01 4.85e+00 angle pdb=" N GLY A 329 " pdb=" CA GLY A 329 " pdb=" C GLY A 329 " ideal model delta sigma weight residual 113.18 108.14 5.04 2.37e+00 1.78e-01 4.52e+00 angle pdb=" CA LEU A 296 " pdb=" CB LEU A 296 " pdb=" CG LEU A 296 " ideal model delta sigma weight residual 116.30 123.72 -7.42 3.50e+00 8.16e-02 4.49e+00 angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 125.38 -3.68 1.80e+00 3.09e-01 4.18e+00 ... (remaining 9224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 3557 15.76 - 31.52: 286 31.52 - 47.27: 60 47.27 - 63.03: 5 63.03 - 78.79: 1 Dihedral angle restraints: 3909 sinusoidal: 1267 harmonic: 2642 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU A 266 " pdb=" C LEU A 266 " pdb=" N GLN A 267 " pdb=" CA GLN A 267 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 704 0.029 - 0.057: 253 0.057 - 0.086: 93 0.086 - 0.115: 44 0.115 - 0.143: 9 Chirality restraints: 1103 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 2.54 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1100 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 174 " 0.010 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR R 174 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR R 174 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 174 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR R 174 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 174 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 174 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 265 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ARG A 265 " -0.023 2.00e-02 2.50e+03 pdb=" O ARG A 265 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 266 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO G 49 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.018 5.00e-02 4.00e+02 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1127 2.76 - 3.30: 6359 3.30 - 3.83: 11208 3.83 - 4.37: 12378 4.37 - 4.90: 22691 Nonbonded interactions: 53763 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.276 3.040 nonbonded pdb=" O SER A 252 " pdb=" OG SER A 252 " model vdw 2.276 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASN R 293 " pdb=" OH TYR R 308 " model vdw 2.281 3.040 ... (remaining 53758 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=0.00 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.054 6752 Z= 0.196 Angle : 0.478 7.417 9229 Z= 0.252 Chirality : 0.038 0.143 1103 Planarity : 0.003 0.033 1161 Dihedral : 12.026 78.790 2190 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.74 (0.28), residues: 890 helix: 2.90 (0.25), residues: 382 sheet: -0.04 (0.41), residues: 162 loop : -0.23 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 105 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.001 PHE B 235 TYR 0.028 0.001 TYR R 174 ARG 0.002 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.785 Fit side-chains REVERT: B 322 ASP cc_start: 0.8137 (m-30) cc_final: 0.7924 (m-30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1900 time to fit residues: 26.3809 Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.0070 chunk 36 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122280 restraints weight = 10159.671| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.06 r_work: 0.3467 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6752 Z= 0.153 Angle : 0.460 5.508 9229 Z= 0.251 Chirality : 0.039 0.143 1103 Planarity : 0.003 0.034 1161 Dihedral : 4.293 21.035 978 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.66 % Allowed : 6.95 % Favored : 91.39 % 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: 1.85 (0.29), residues: 890 helix: 2.73 (0.25), residues: 397 sheet: 0.14 (0.41), residues: 166 loop : -0.03 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE R 289 TYR 0.009 0.001 TYR B 124 ARG 0.001 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.695 Fit side-chains REVERT: B 322 ASP cc_start: 0.8303 (m-30) cc_final: 0.8054 (m-30) REVERT: R 180 GLU cc_start: 0.7766 (tp30) cc_final: 0.7539 (tp30) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.1786 time to fit residues: 25.1125 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain R residue 220 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122338 restraints weight = 10457.414| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.14 r_work: 0.3440 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6752 Z= 0.182 Angle : 0.453 5.629 9229 Z= 0.246 Chirality : 0.039 0.140 1103 Planarity : 0.003 0.034 1161 Dihedral : 4.234 19.384 978 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.82 % Allowed : 10.10 % Favored : 88.08 % 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: 1.81 (0.29), residues: 890 helix: 2.80 (0.25), residues: 390 sheet: 0.02 (0.40), residues: 171 loop : -0.06 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.010 0.001 PHE R 289 TYR 0.018 0.001 TYR R 174 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.691 Fit side-chains REVERT: B 322 ASP cc_start: 0.8322 (m-30) cc_final: 0.8121 (m-30) REVERT: R 84 LEU cc_start: 0.8601 (mt) cc_final: 0.8376 (mt) REVERT: R 180 GLU cc_start: 0.7775 (tp30) cc_final: 0.7485 (tp30) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.1778 time to fit residues: 25.0410 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117402 restraints weight = 10590.168| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.10 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6752 Z= 0.261 Angle : 0.482 5.742 9229 Z= 0.262 Chirality : 0.040 0.135 1103 Planarity : 0.003 0.036 1161 Dihedral : 4.384 21.165 978 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.65 % Allowed : 11.59 % Favored : 85.76 % 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: 1.65 (0.29), residues: 890 helix: 2.63 (0.25), residues: 397 sheet: -0.12 (0.40), residues: 166 loop : -0.12 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS B 183 PHE 0.013 0.001 PHE R 289 TYR 0.021 0.001 TYR R 174 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.756 Fit side-chains REVERT: A 297 LEU cc_start: 0.9203 (tp) cc_final: 0.8881 (tt) REVERT: B 322 ASP cc_start: 0.8373 (m-30) cc_final: 0.8135 (m-30) REVERT: R 36 MET cc_start: 0.7469 (mtp) cc_final: 0.7200 (ttm) REVERT: R 65 GLN cc_start: 0.8696 (mt0) cc_final: 0.7946 (mp10) REVERT: R 84 LEU cc_start: 0.8656 (mt) cc_final: 0.8425 (mt) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.1716 time to fit residues: 23.8193 Evaluate side-chains 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117655 restraints weight = 10524.178| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.23 r_work: 0.3393 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6752 Z= 0.208 Angle : 0.470 5.902 9229 Z= 0.254 Chirality : 0.039 0.136 1103 Planarity : 0.003 0.033 1161 Dihedral : 4.315 21.224 978 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.65 % Allowed : 11.92 % Favored : 85.43 % 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: 1.63 (0.29), residues: 890 helix: 2.68 (0.25), residues: 396 sheet: -0.29 (0.40), residues: 168 loop : -0.14 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE R 289 TYR 0.015 0.001 TYR R 174 ARG 0.001 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.701 Fit side-chains REVERT: B 322 ASP cc_start: 0.8387 (m-30) cc_final: 0.8164 (m-30) REVERT: R 84 LEU cc_start: 0.8638 (mt) cc_final: 0.8405 (mt) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1853 time to fit residues: 25.0249 Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119494 restraints weight = 10541.949| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.12 r_work: 0.3399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6752 Z= 0.216 Angle : 0.474 6.307 9229 Z= 0.255 Chirality : 0.040 0.136 1103 Planarity : 0.003 0.033 1161 Dihedral : 4.312 21.261 978 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.81 % Allowed : 12.58 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 890 helix: 2.66 (0.25), residues: 396 sheet: -0.42 (0.38), residues: 175 loop : -0.08 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE R 289 TYR 0.012 0.001 TYR R 174 ARG 0.001 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.630 Fit side-chains REVERT: B 183 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7906 (t-90) REVERT: B 293 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8679 (p0) REVERT: B 322 ASP cc_start: 0.8366 (m-30) cc_final: 0.8161 (m-30) REVERT: R 84 LEU cc_start: 0.8633 (mt) cc_final: 0.8401 (mt) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.1606 time to fit residues: 22.7088 Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120629 restraints weight = 10430.547| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.12 r_work: 0.3416 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6752 Z= 0.178 Angle : 0.463 6.705 9229 Z= 0.248 Chirality : 0.039 0.135 1103 Planarity : 0.003 0.032 1161 Dihedral : 4.240 21.062 978 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.81 % Allowed : 13.58 % Favored : 83.61 % 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: 1.61 (0.29), residues: 890 helix: 2.72 (0.25), residues: 396 sheet: -0.44 (0.38), residues: 175 loop : -0.11 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE R 289 TYR 0.010 0.001 TYR R 174 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.661 Fit side-chains REVERT: B 183 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7847 (t-90) REVERT: B 293 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8534 (p0) REVERT: R 65 GLN cc_start: 0.8764 (mt0) cc_final: 0.7926 (mp10) REVERT: R 84 LEU cc_start: 0.8617 (mt) cc_final: 0.8386 (mt) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1649 time to fit residues: 22.8641 Evaluate side-chains 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120126 restraints weight = 10534.220| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.13 r_work: 0.3414 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6752 Z= 0.203 Angle : 0.474 6.965 9229 Z= 0.253 Chirality : 0.039 0.135 1103 Planarity : 0.003 0.032 1161 Dihedral : 4.242 21.215 978 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.81 % Allowed : 13.08 % Favored : 84.11 % 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: 1.58 (0.29), residues: 890 helix: 2.69 (0.25), residues: 396 sheet: -0.45 (0.39), residues: 175 loop : -0.12 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE R 289 TYR 0.010 0.001 TYR R 199 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.715 Fit side-chains REVERT: B 183 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: B 293 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (p0) REVERT: R 84 LEU cc_start: 0.8634 (mt) cc_final: 0.8408 (mt) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.1617 time to fit residues: 22.5986 Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119288 restraints weight = 10612.259| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.15 r_work: 0.3395 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6752 Z= 0.233 Angle : 0.498 11.361 9229 Z= 0.262 Chirality : 0.040 0.135 1103 Planarity : 0.003 0.032 1161 Dihedral : 4.296 21.527 978 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.48 % Allowed : 13.91 % Favored : 83.61 % 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: 890 helix: 2.64 (0.25), residues: 396 sheet: -0.51 (0.39), residues: 175 loop : -0.13 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE R 289 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.732 Fit side-chains REVERT: B 183 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7914 (t-90) REVERT: R 65 GLN cc_start: 0.8768 (mt0) cc_final: 0.7967 (mp10) REVERT: R 84 LEU cc_start: 0.8627 (mt) cc_final: 0.8399 (mt) outliers start: 15 outliers final: 13 residues processed: 99 average time/residue: 0.1765 time to fit residues: 23.8546 Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 0.0980 chunk 20 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 87 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120499 restraints weight = 10605.937| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.25 r_work: 0.3442 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6752 Z= 0.143 Angle : 0.470 11.068 9229 Z= 0.245 Chirality : 0.038 0.135 1103 Planarity : 0.003 0.031 1161 Dihedral : 4.096 21.085 978 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.15 % Allowed : 14.24 % Favored : 83.61 % 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: 1.68 (0.29), residues: 890 helix: 2.81 (0.25), residues: 395 sheet: -0.43 (0.39), residues: 175 loop : -0.11 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE R 290 TYR 0.008 0.001 TYR R 174 ARG 0.002 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.666 Fit side-chains REVERT: B 183 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7582 (t-90) REVERT: R 65 GLN cc_start: 0.8787 (mt0) cc_final: 0.7979 (mp10) REVERT: R 84 LEU cc_start: 0.8572 (mt) cc_final: 0.8344 (mt) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.1731 time to fit residues: 24.2713 Evaluate side-chains 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.3980 chunk 74 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122193 restraints weight = 10625.809| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.17 r_work: 0.3434 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6752 Z= 0.164 Angle : 0.473 10.930 9229 Z= 0.248 Chirality : 0.039 0.135 1103 Planarity : 0.003 0.031 1161 Dihedral : 4.077 20.893 978 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.82 % Allowed : 14.90 % Favored : 83.28 % 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: 1.68 (0.29), residues: 890 helix: 2.83 (0.25), residues: 396 sheet: -0.49 (0.39), residues: 177 loop : -0.10 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE R 289 TYR 0.009 0.001 TYR R 199 ARG 0.002 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.52 seconds wall clock time: 59 minutes 51.19 seconds (3591.19 seconds total)