Starting phenix.real_space_refine on Tue Mar 3 16:28:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mby_23750/03_2026/7mby_23750.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.032 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 57 5.16 5 C 4416 2.51 5 N 1164 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6881 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2501 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2250 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 6881 At special positions: 0 Unit cell: (73.45, 102.7, 121.55, 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 57 16.00 O 1244 8.00 N 1164 7.00 C 4416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 166.9 milliseconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 47.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.561A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.614A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 removed outlier: 4.052A pdb=" N VAL R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 95 removed outlier: 3.838A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 105 Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.511A pdb=" N GLY R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 removed outlier: 4.334A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 4.270A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 218 removed outlier: 3.539A pdb=" N SER R 208 " --> pdb=" O VAL R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 238 removed outlier: 3.978A pdb=" N MET R 226 " --> pdb=" O GLY R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 339 removed outlier: 3.547A pdb=" N ARG R 313 " --> pdb=" O LYS R 309 " (cutoff:3.500A) Proline residue: R 328 - end of helix removed outlier: 3.644A pdb=" N TYR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 347 removed outlier: 3.930A pdb=" N ALA R 343 " --> pdb=" O ASP R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 removed outlier: 3.511A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.541A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.147A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.506A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.877A 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 293 through 303 removed outlier: 3.767A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.172A 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 352 removed outlier: 4.946A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.014A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.568A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.516A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.668A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.512A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 186 removed outlier: 3.599A pdb=" N ASN R 181 " --> pdb=" O ARG R 197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG R 197 " --> pdb=" O ASN R 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.916A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1113 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: 1.10 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1095 1.31 - 1.44: 1909 1.44 - 1.56: 3926 1.56 - 1.69: 6 1.69 - 1.82: 84 Bond restraints: 7020 Sorted by residual: bond pdb=" CAI Y01 R 501 " pdb=" CAK Y01 R 501 " ideal model delta sigma weight residual 1.492 1.582 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CAZ Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sigma weight residual 1.519 1.441 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CAK Y01 R 501 " pdb=" CBD Y01 R 501 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CAP Y01 R 501 " pdb=" CAQ Y01 R 501 " ideal model delta sigma weight residual 1.541 1.610 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CAY Y01 R 501 " pdb=" OAW Y01 R 501 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 9366 2.90 - 5.81: 147 5.81 - 8.71: 23 8.71 - 11.62: 4 11.62 - 14.52: 1 Bond angle restraints: 9541 Sorted by residual: angle pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta sigma weight residual 110.79 100.70 10.09 1.68e+00 3.54e-01 3.61e+01 angle pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 115.16 100.64 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 125.66 132.89 -7.23 1.85e+00 2.92e-01 1.53e+01 angle pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 100.21 111.53 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLY B 319 " pdb=" C GLY B 319 " pdb=" O GLY B 319 " ideal model delta sigma weight residual 121.19 117.83 3.36 9.10e-01 1.21e+00 1.36e+01 ... (remaining 9536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 4005 21.72 - 43.44: 176 43.44 - 65.15: 18 65.15 - 86.87: 7 86.87 - 108.59: 1 Dihedral angle restraints: 4207 sinusoidal: 1603 harmonic: 2604 Sorted by residual: dihedral pdb=" C ARG R 376 " pdb=" N ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual -122.60 -108.99 -13.61 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" CBC Y01 R 501 " pdb=" CAR Y01 R 501 " pdb=" CAT Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sinusoidal sigma weight residual -57.13 51.46 -108.59 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual 122.80 114.15 8.65 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 941 0.079 - 0.158: 161 0.158 - 0.236: 14 0.236 - 0.315: 3 0.315 - 0.394: 4 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CBG Y01 R 501 " pdb=" CAQ Y01 R 501 " pdb=" CBD Y01 R 501 " pdb=" CBI Y01 R 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ARG R 376 " pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CB ARG R 376 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1120 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 200 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO R 201 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 174 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO R 175 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 152 " -0.018 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" CG TRP R 152 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 152 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 152 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 152 " -0.001 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1752 2.80 - 3.33: 6294 3.33 - 3.85: 11771 3.85 - 4.38: 13697 4.38 - 4.90: 23660 Nonbonded interactions: 57174 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.319 3.040 nonbonded pdb=" O CYS R 114 " pdb=" OG1 THR R 118 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.346 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.354 3.040 ... (remaining 57169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.006 0.101 7022 Z= 0.305 Angle : 0.946 14.524 9543 Z= 0.504 Chirality : 0.061 0.394 1123 Planarity : 0.007 0.077 1189 Dihedral : 12.467 108.587 2506 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.26), residues: 869 helix: -0.90 (0.23), residues: 383 sheet: 0.10 (0.39), residues: 185 loop : -1.52 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 342 TYR 0.037 0.003 TYR B 59 PHE 0.023 0.003 PHE B 151 TRP 0.038 0.004 TRP R 152 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 7020) covalent geometry : angle 0.94574 ( 9541) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.48947 ( 2) hydrogen bonds : bond 0.23804 ( 381) hydrogen bonds : angle 7.68792 ( 1113) Misc. bond : bond 0.10098 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7137 (mmp-170) REVERT: B 65 THR cc_start: 0.7138 (m) cc_final: 0.6775 (p) REVERT: B 217 MET cc_start: 0.7681 (ptt) cc_final: 0.6510 (ptt) REVERT: B 269 ILE cc_start: 0.5407 (mm) cc_final: 0.4956 (mt) REVERT: R 105 LYS cc_start: 0.8712 (mttp) cc_final: 0.8509 (mtmt) REVERT: R 126 SER cc_start: 0.8362 (t) cc_final: 0.7868 (p) REVERT: R 145 LYS cc_start: 0.7389 (pttt) cc_final: 0.7160 (pttp) REVERT: R 195 MET cc_start: 0.7015 (mtm) cc_final: 0.6807 (mtt) REVERT: A 25 MET cc_start: 0.6445 (ttm) cc_final: 0.5929 (ttm) REVERT: A 36 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 218 ASN cc_start: 0.7201 (t0) cc_final: 0.6513 (m-40) REVERT: A 253 TYR cc_start: 0.7023 (m-80) cc_final: 0.6536 (m-80) REVERT: A 343 LYS cc_start: 0.6797 (tmtt) cc_final: 0.6445 (tptp) REVERT: A 347 ASP cc_start: 0.4691 (p0) cc_final: 0.4244 (p0) REVERT: A 380 LYS cc_start: 0.7234 (tmtt) cc_final: 0.6851 (tttm) outliers start: 0 outliers final: 1 residues processed: 186 average time/residue: 0.5085 time to fit residues: 99.6474 Evaluate side-chains 102 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 98 ASN R 191 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.151751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.124993 restraints weight = 14741.136| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.84 r_work: 0.4012 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7022 Z= 0.251 Angle : 0.762 9.916 9543 Z= 0.398 Chirality : 0.048 0.172 1123 Planarity : 0.006 0.064 1189 Dihedral : 6.910 54.714 1025 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.33 % Allowed : 14.17 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 869 helix: 0.81 (0.26), residues: 381 sheet: -0.21 (0.38), residues: 188 loop : -1.25 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.013 0.002 TYR R 237 PHE 0.030 0.003 PHE A 219 TRP 0.016 0.003 TRP B 297 HIS 0.011 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 7020) covalent geometry : angle 0.76191 ( 9541) SS BOND : bond 0.00211 ( 1) SS BOND : angle 1.97604 ( 2) hydrogen bonds : bond 0.05625 ( 381) hydrogen bonds : angle 5.20553 ( 1113) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.8523 (ptt) cc_final: 0.8299 (ptt) REVERT: B 234 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.4484 (t80) REVERT: G 32 LYS cc_start: 0.8532 (tmtp) cc_final: 0.8329 (tptp) REVERT: R 72 MET cc_start: 0.7732 (ttp) cc_final: 0.7529 (ptp) REVERT: R 92 LEU cc_start: 0.7606 (mt) cc_final: 0.7215 (mp) REVERT: R 105 LYS cc_start: 0.8753 (mttp) cc_final: 0.8413 (mtmt) REVERT: R 126 SER cc_start: 0.8282 (t) cc_final: 0.7928 (p) REVERT: R 187 LYS cc_start: 0.5814 (mttt) cc_final: 0.5610 (mptt) REVERT: A 35 GLU cc_start: 0.7127 (pp20) cc_final: 0.6806 (mt-10) REVERT: A 218 ASN cc_start: 0.7213 (t0) cc_final: 0.6436 (m-40) REVERT: A 380 LYS cc_start: 0.7343 (tmtt) cc_final: 0.6799 (tptt) outliers start: 24 outliers final: 12 residues processed: 129 average time/residue: 0.5254 time to fit residues: 71.5138 Evaluate side-chains 109 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.127834 restraints weight = 14490.165| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.81 r_work: 0.4069 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7022 Z= 0.139 Angle : 0.652 12.629 9543 Z= 0.331 Chirality : 0.044 0.156 1123 Planarity : 0.004 0.049 1189 Dihedral : 6.015 59.576 1023 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.06 % Allowed : 17.64 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 869 helix: 1.44 (0.27), residues: 382 sheet: -0.24 (0.37), residues: 192 loop : -1.07 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.020 0.002 TYR A 360 PHE 0.018 0.001 PHE A 219 TRP 0.016 0.002 TRP R 326 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7020) covalent geometry : angle 0.65172 ( 9541) SS BOND : bond 0.00364 ( 1) SS BOND : angle 1.97669 ( 2) hydrogen bonds : bond 0.04650 ( 381) hydrogen bonds : angle 4.78945 ( 1113) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.4709 (t80) REVERT: G 37 LEU cc_start: 0.7130 (mm) cc_final: 0.6899 (mm) REVERT: R 126 SER cc_start: 0.8268 (t) cc_final: 0.7940 (p) REVERT: R 368 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8289 (pp) REVERT: R 373 MET cc_start: 0.7744 (mtp) cc_final: 0.7234 (tmt) REVERT: A 275 SER cc_start: 0.7704 (OUTLIER) cc_final: 0.7386 (t) REVERT: A 380 LYS cc_start: 0.7331 (tmtt) cc_final: 0.6754 (tptt) REVERT: A 390 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 22 outliers final: 8 residues processed: 119 average time/residue: 0.5252 time to fit residues: 65.9154 Evaluate side-chains 101 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 368 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** 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 = 0.4492 r_free = 0.4492 target = 0.151365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.125025 restraints weight = 14748.411| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.82 r_work: 0.4024 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7022 Z= 0.185 Angle : 0.694 10.681 9543 Z= 0.350 Chirality : 0.045 0.159 1123 Planarity : 0.004 0.059 1189 Dihedral : 5.967 58.055 1023 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.31 % Allowed : 16.67 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.29), residues: 869 helix: 1.54 (0.27), residues: 383 sheet: -0.38 (0.37), residues: 192 loop : -1.07 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.014 0.002 TYR R 176 PHE 0.016 0.002 PHE A 219 TRP 0.018 0.002 TRP R 326 HIS 0.007 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7020) covalent geometry : angle 0.69318 ( 9541) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.84066 ( 2) hydrogen bonds : bond 0.04656 ( 381) hydrogen bonds : angle 4.83021 ( 1113) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: B 234 PHE cc_start: 0.5673 (OUTLIER) cc_final: 0.4769 (t80) REVERT: B 269 ILE cc_start: 0.5232 (mm) cc_final: 0.4843 (mt) REVERT: B 293 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7002 (t0) REVERT: R 72 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7480 (ptt) REVERT: R 92 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7143 (mp) REVERT: R 126 SER cc_start: 0.8347 (t) cc_final: 0.8025 (p) REVERT: R 368 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8319 (pp) REVERT: R 373 MET cc_start: 0.7733 (mtp) cc_final: 0.7299 (tmt) REVERT: A 380 LYS cc_start: 0.7330 (tmtt) cc_final: 0.6757 (tptt) REVERT: A 390 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8093 (tm-30) outliers start: 31 outliers final: 12 residues processed: 117 average time/residue: 0.4617 time to fit residues: 57.4238 Evaluate side-chains 106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 368 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 98 ASN ** A 362 HIS ** 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 = 0.4528 r_free = 0.4528 target = 0.153851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.128187 restraints weight = 14770.052| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.86 r_work: 0.4080 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7022 Z= 0.128 Angle : 0.657 10.512 9543 Z= 0.327 Chirality : 0.043 0.159 1123 Planarity : 0.004 0.056 1189 Dihedral : 5.731 57.292 1023 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.89 % Allowed : 18.47 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.29), residues: 869 helix: 1.73 (0.27), residues: 385 sheet: -0.30 (0.37), residues: 192 loop : -1.02 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.046 0.002 TYR R 176 PHE 0.012 0.001 PHE A 219 TRP 0.021 0.002 TRP R 326 HIS 0.007 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7020) covalent geometry : angle 0.65595 ( 9541) SS BOND : bond 0.00610 ( 1) SS BOND : angle 2.04380 ( 2) hydrogen bonds : bond 0.04115 ( 381) hydrogen bonds : angle 4.63706 ( 1113) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5536 (OUTLIER) cc_final: 0.5023 (t80) REVERT: B 293 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.7029 (t0) REVERT: G 37 LEU cc_start: 0.7013 (mm) cc_final: 0.6754 (mm) REVERT: R 92 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7114 (mp) REVERT: R 126 SER cc_start: 0.8252 (t) cc_final: 0.7741 (p) REVERT: R 130 PHE cc_start: 0.8503 (m-10) cc_final: 0.8275 (m-80) REVERT: R 306 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4631 (pp-130) REVERT: R 329 ILE cc_start: 0.7985 (tp) cc_final: 0.7660 (mp) REVERT: R 368 ILE cc_start: 0.8699 (pt) cc_final: 0.8342 (pp) REVERT: A 336 ARG cc_start: 0.3855 (OUTLIER) cc_final: 0.3385 (tpt-90) REVERT: A 380 LYS cc_start: 0.7264 (tmtt) cc_final: 0.6689 (tptt) REVERT: A 390 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8048 (tm-30) outliers start: 28 outliers final: 13 residues processed: 116 average time/residue: 0.4736 time to fit residues: 58.4761 Evaluate side-chains 104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 336 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** 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 = 0.4542 r_free = 0.4542 target = 0.154690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.129179 restraints weight = 14709.932| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.82 r_work: 0.4094 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7022 Z= 0.124 Angle : 0.641 9.574 9543 Z= 0.322 Chirality : 0.043 0.154 1123 Planarity : 0.004 0.055 1189 Dihedral : 5.619 56.219 1023 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.89 % Allowed : 20.00 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 869 helix: 1.86 (0.27), residues: 384 sheet: -0.35 (0.37), residues: 196 loop : -0.92 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 310 TYR 0.017 0.001 TYR A 360 PHE 0.010 0.001 PHE B 151 TRP 0.023 0.002 TRP R 326 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7020) covalent geometry : angle 0.64066 ( 9541) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.90231 ( 2) hydrogen bonds : bond 0.03945 ( 381) hydrogen bonds : angle 4.55948 ( 1113) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: B 234 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4895 (t80) REVERT: B 293 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6648 (t0) REVERT: G 37 LEU cc_start: 0.6902 (mm) cc_final: 0.6612 (mm) REVERT: R 92 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7061 (mp) REVERT: R 126 SER cc_start: 0.8303 (t) cc_final: 0.7893 (p) REVERT: R 155 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6369 (mptp) REVERT: R 205 MET cc_start: 0.3410 (ptt) cc_final: 0.2667 (pmm) REVERT: R 235 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7138 (mp0) REVERT: R 306 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4777 (pp-130) REVERT: R 329 ILE cc_start: 0.7962 (tp) cc_final: 0.7659 (mp) REVERT: A 252 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6724 (p0) REVERT: A 253 TYR cc_start: 0.7270 (m-80) cc_final: 0.6989 (m-80) REVERT: A 380 LYS cc_start: 0.7285 (tmtt) cc_final: 0.6704 (tptt) REVERT: A 390 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8032 (tm-30) outliers start: 28 outliers final: 11 residues processed: 110 average time/residue: 0.4871 time to fit residues: 56.9238 Evaluate side-chains 110 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN A 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.155335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.129578 restraints weight = 14617.068| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.81 r_work: 0.4104 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7022 Z= 0.130 Angle : 0.657 9.151 9543 Z= 0.332 Chirality : 0.044 0.160 1123 Planarity : 0.004 0.056 1189 Dihedral : 5.573 55.367 1023 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.17 % Allowed : 19.72 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.29), residues: 869 helix: 1.79 (0.27), residues: 384 sheet: -0.40 (0.37), residues: 196 loop : -0.89 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 336 TYR 0.037 0.001 TYR R 176 PHE 0.015 0.001 PHE R 130 TRP 0.028 0.002 TRP R 326 HIS 0.005 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7020) covalent geometry : angle 0.65657 ( 9541) SS BOND : bond 0.00385 ( 1) SS BOND : angle 1.98390 ( 2) hydrogen bonds : bond 0.04054 ( 381) hydrogen bonds : angle 4.55101 ( 1113) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: B 234 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.4925 (t80) REVERT: R 126 SER cc_start: 0.8273 (t) cc_final: 0.7079 (p) REVERT: R 130 PHE cc_start: 0.8452 (m-80) cc_final: 0.7863 (m-80) REVERT: R 155 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6366 (mptp) REVERT: R 205 MET cc_start: 0.3129 (ptt) cc_final: 0.2480 (pmm) REVERT: R 306 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4784 (pp-130) REVERT: R 329 ILE cc_start: 0.7937 (tp) cc_final: 0.7613 (mp) REVERT: A 252 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6699 (p0) REVERT: A 253 TYR cc_start: 0.7273 (m-80) cc_final: 0.6846 (m-80) REVERT: A 380 LYS cc_start: 0.7286 (tmtt) cc_final: 0.6885 (ttpt) REVERT: A 390 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8014 (tm-30) outliers start: 30 outliers final: 15 residues processed: 114 average time/residue: 0.4485 time to fit residues: 54.5336 Evaluate side-chains 111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN A 236 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.153167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.127064 restraints weight = 14914.052| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.85 r_work: 0.4069 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7022 Z= 0.155 Angle : 0.716 10.434 9543 Z= 0.356 Chirality : 0.045 0.216 1123 Planarity : 0.004 0.056 1189 Dihedral : 5.674 54.672 1023 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 22.50 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 869 helix: 1.77 (0.27), residues: 381 sheet: -0.41 (0.38), residues: 192 loop : -0.95 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 310 TYR 0.029 0.002 TYR R 176 PHE 0.045 0.002 PHE R 93 TRP 0.031 0.002 TRP R 326 HIS 0.003 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7020) covalent geometry : angle 0.71510 ( 9541) SS BOND : bond 0.00365 ( 1) SS BOND : angle 2.21927 ( 2) hydrogen bonds : bond 0.04153 ( 381) hydrogen bonds : angle 4.61049 ( 1113) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.278 Fit side-chains REVERT: B 59 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: B 217 MET cc_start: 0.8284 (ptt) cc_final: 0.7982 (ttt) REVERT: B 234 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.4894 (t80) REVERT: G 38 MET cc_start: 0.6977 (tpt) cc_final: 0.6092 (tpt) REVERT: G 42 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7775 (mt-10) REVERT: R 126 SER cc_start: 0.8267 (t) cc_final: 0.7107 (p) REVERT: R 130 PHE cc_start: 0.8475 (m-80) cc_final: 0.7886 (m-80) REVERT: R 155 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6440 (mptp) REVERT: R 187 LYS cc_start: 0.5060 (mtpt) cc_final: 0.4264 (mptm) REVERT: R 235 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7127 (mp0) REVERT: R 306 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4804 (pp-130) REVERT: R 329 ILE cc_start: 0.7958 (tp) cc_final: 0.7619 (mp) REVERT: R 382 MET cc_start: 0.8837 (pp-130) cc_final: 0.8441 (mmt) REVERT: A 252 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6690 (p0) REVERT: A 253 TYR cc_start: 0.7323 (m-80) cc_final: 0.7037 (m-80) REVERT: A 380 LYS cc_start: 0.7264 (tmtt) cc_final: 0.6682 (tptt) REVERT: A 390 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 0.5104 time to fit residues: 58.3846 Evaluate side-chains 106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 0.0040 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.155473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.129833 restraints weight = 14822.292| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.83 r_work: 0.4109 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7022 Z= 0.132 Angle : 0.719 11.322 9543 Z= 0.359 Chirality : 0.044 0.236 1123 Planarity : 0.004 0.057 1189 Dihedral : 5.586 54.576 1023 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 23.33 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.29), residues: 869 helix: 1.82 (0.27), residues: 379 sheet: -0.46 (0.38), residues: 191 loop : -0.86 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.028 0.001 TYR R 176 PHE 0.037 0.002 PHE R 93 TRP 0.034 0.002 TRP R 326 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7020) covalent geometry : angle 0.71795 ( 9541) SS BOND : bond 0.00443 ( 1) SS BOND : angle 2.13128 ( 2) hydrogen bonds : bond 0.04028 ( 381) hydrogen bonds : angle 4.56523 ( 1113) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.287 Fit side-chains REVERT: B 42 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7228 (tpp-160) REVERT: B 59 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: B 217 MET cc_start: 0.8232 (ptt) cc_final: 0.7941 (ttt) REVERT: B 234 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5071 (t80) REVERT: G 38 MET cc_start: 0.6932 (tpt) cc_final: 0.5917 (tpt) REVERT: G 42 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7701 (mt-10) REVERT: R 126 SER cc_start: 0.8278 (t) cc_final: 0.7166 (p) REVERT: R 130 PHE cc_start: 0.8472 (m-80) cc_final: 0.7947 (m-80) REVERT: R 187 LYS cc_start: 0.5034 (mtpt) cc_final: 0.4241 (mptm) REVERT: R 306 MET cc_start: 0.5351 (OUTLIER) cc_final: 0.4943 (pp-130) REVERT: R 329 ILE cc_start: 0.7923 (tp) cc_final: 0.7587 (mp) REVERT: R 382 MET cc_start: 0.8821 (pp-130) cc_final: 0.8449 (mmt) REVERT: A 35 GLU cc_start: 0.6709 (pp20) cc_final: 0.6494 (pt0) REVERT: A 236 GLN cc_start: 0.8085 (mt0) cc_final: 0.7880 (mt0) REVERT: A 252 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6710 (p0) REVERT: A 253 TYR cc_start: 0.7320 (m-80) cc_final: 0.6877 (m-80) REVERT: A 380 LYS cc_start: 0.7246 (tmtt) cc_final: 0.6863 (ttpt) REVERT: A 390 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8031 (tm-30) outliers start: 20 outliers final: 10 residues processed: 98 average time/residue: 0.5039 time to fit residues: 52.5276 Evaluate side-chains 100 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.152124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.126086 restraints weight = 14980.277| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.83 r_work: 0.4052 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7022 Z= 0.172 Angle : 0.759 12.388 9543 Z= 0.378 Chirality : 0.046 0.221 1123 Planarity : 0.004 0.057 1189 Dihedral : 5.741 55.277 1023 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.78 % Allowed : 22.92 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 869 helix: 1.71 (0.27), residues: 381 sheet: -0.62 (0.38), residues: 186 loop : -0.84 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 280 TYR 0.029 0.002 TYR R 176 PHE 0.038 0.002 PHE R 93 TRP 0.038 0.002 TRP R 326 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7020) covalent geometry : angle 0.75883 ( 9541) SS BOND : bond 0.00321 ( 1) SS BOND : angle 2.01623 ( 2) hydrogen bonds : bond 0.04293 ( 381) hydrogen bonds : angle 4.74537 ( 1113) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.289 Fit side-chains REVERT: B 42 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7157 (tpp-160) REVERT: B 59 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: B 234 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.4961 (t80) REVERT: G 38 MET cc_start: 0.7030 (tpt) cc_final: 0.6072 (tpt) REVERT: G 42 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7778 (mt-10) REVERT: R 126 SER cc_start: 0.8325 (t) cc_final: 0.7203 (p) REVERT: R 130 PHE cc_start: 0.8471 (m-80) cc_final: 0.7940 (m-80) REVERT: R 306 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4969 (pp-130) REVERT: R 329 ILE cc_start: 0.7934 (tp) cc_final: 0.7598 (mp) REVERT: R 382 MET cc_start: 0.8837 (pp-130) cc_final: 0.8435 (mmt) REVERT: A 252 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6645 (p0) REVERT: A 253 TYR cc_start: 0.7359 (m-80) cc_final: 0.7124 (m-80) REVERT: A 380 LYS cc_start: 0.7282 (tmtt) cc_final: 0.6831 (tttm) REVERT: A 390 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8067 (tm-30) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.4763 time to fit residues: 49.6402 Evaluate side-chains 98 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.152302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.126060 restraints weight = 14854.150| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.81 r_work: 0.4055 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 7022 Z= 0.349 Angle : 1.122 59.010 9543 Z= 0.646 Chirality : 0.047 0.458 1123 Planarity : 0.005 0.055 1189 Dihedral : 5.886 55.300 1023 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 2.64 % Allowed : 22.78 % Favored : 74.58 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 869 helix: 1.71 (0.27), residues: 381 sheet: -0.63 (0.38), residues: 186 loop : -0.82 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.027 0.002 TYR R 176 PHE 0.033 0.002 PHE R 93 TRP 0.031 0.002 TRP R 326 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 7020) covalent geometry : angle 1.12226 ( 9541) SS BOND : bond 0.00451 ( 1) SS BOND : angle 1.92407 ( 2) hydrogen bonds : bond 0.04275 ( 381) hydrogen bonds : angle 4.74958 ( 1113) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.43 seconds wall clock time: 60 minutes 5.18 seconds (3605.18 seconds total)