Starting phenix.real_space_refine on Fri Jul 25 04:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_23750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_23750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_23750.map" model { file = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_23750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2025/7mby_23750.cif" } resolution = 2.44 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= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, '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, 'ARG:plan': 1, 'TRP: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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} 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: 4.44, per 1000 atoms: 0.65 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: 1.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.12 Time building geometry restraints manager: 1.83 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: 2.250 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.030 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- 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 : 4.92 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 (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: -1.45 (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 TRP 0.038 0.004 TRP R 152 HIS 0.007 0.002 HIS A 357 PHE 0.023 0.003 PHE B 151 TYR 0.037 0.003 TYR B 59 ARG 0.016 0.001 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.23804 ( 381) hydrogen bonds : angle 7.68792 ( 1113) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.48947 ( 2) covalent geometry : bond 0.00586 ( 7020) covalent geometry : angle 0.94574 ( 9541) 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 : 0.845 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: 1.1321 time to fit residues: 222.3141 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 : 0.783 ------------------------------------------------------------------------------- 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 72 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 259 GLN R 98 ASN R 191 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 292 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.157469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.131476 restraints weight = 14468.387| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.88 r_work: 0.4120 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7022 Z= 0.152 Angle : 0.677 8.266 9543 Z= 0.350 Chirality : 0.045 0.174 1123 Planarity : 0.005 0.064 1189 Dihedral : 6.685 52.689 1025 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.22 % Allowed : 14.17 % 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: -0.09 (0.28), residues: 869 helix: 0.90 (0.26), residues: 386 sheet: -0.01 (0.38), residues: 189 loop : -1.30 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 297 HIS 0.008 0.001 HIS A 362 PHE 0.028 0.002 PHE A 219 TYR 0.010 0.002 TYR R 237 ARG 0.006 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 381) hydrogen bonds : angle 4.95052 ( 1113) SS BOND : bond 0.00349 ( 1) SS BOND : angle 2.00269 ( 2) covalent geometry : bond 0.00328 ( 7020) covalent geometry : angle 0.67672 ( 9541) Misc. bond : bond 0.00010 ( 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 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8442 (ptt) cc_final: 0.8154 (ptt) REVERT: B 234 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4742 (t80) REVERT: B 269 ILE cc_start: 0.5375 (mm) cc_final: 0.4826 (mt) REVERT: G 37 LEU cc_start: 0.7150 (mm) cc_final: 0.6942 (mm) REVERT: R 92 LEU cc_start: 0.7556 (mt) cc_final: 0.7208 (mp) REVERT: R 105 LYS cc_start: 0.8699 (mttp) cc_final: 0.8356 (mtmt) REVERT: R 126 SER cc_start: 0.8280 (t) cc_final: 0.7999 (p) REVERT: R 220 ILE cc_start: 0.7953 (mm) cc_final: 0.7493 (mt) REVERT: A 39 ARG cc_start: 0.5964 (mtt-85) cc_final: 0.5299 (mtm-85) REVERT: A 218 ASN cc_start: 0.7124 (t0) cc_final: 0.6445 (m-40) REVERT: A 253 TYR cc_start: 0.7283 (m-80) cc_final: 0.6564 (m-80) REVERT: A 380 LYS cc_start: 0.7350 (tmtt) cc_final: 0.6965 (ttpt) REVERT: A 390 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8046 (tm-30) outliers start: 16 outliers final: 5 residues processed: 128 average time/residue: 1.1350 time to fit residues: 153.5731 Evaluate side-chains 102 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** 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 = 0.4507 r_free = 0.4507 target = 0.152492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.126432 restraints weight = 14651.926| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.84 r_work: 0.4043 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7022 Z= 0.189 Angle : 0.699 12.820 9543 Z= 0.353 Chirality : 0.045 0.155 1123 Planarity : 0.004 0.049 1189 Dihedral : 6.054 59.448 1023 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.75 % Allowed : 16.81 % Favored : 79.44 % 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: 0.29 (0.29), residues: 869 helix: 1.49 (0.27), residues: 379 sheet: -0.33 (0.37), residues: 193 loop : -1.09 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 326 HIS 0.008 0.002 HIS A 357 PHE 0.025 0.002 PHE A 219 TYR 0.025 0.002 TYR A 360 ARG 0.006 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 381) hydrogen bonds : angle 4.83716 ( 1113) SS BOND : bond 0.00906 ( 1) SS BOND : angle 1.60032 ( 2) covalent geometry : bond 0.00426 ( 7020) covalent geometry : angle 0.69879 ( 9541) Misc. bond : bond 0.00015 ( 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 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4625 (t80) REVERT: B 269 ILE cc_start: 0.5283 (mm) cc_final: 0.4703 (mt) REVERT: R 105 LYS cc_start: 0.8683 (mttp) cc_final: 0.8427 (mtmt) REVERT: R 126 SER cc_start: 0.8279 (t) cc_final: 0.7954 (p) REVERT: A 380 LYS cc_start: 0.7341 (tmtt) cc_final: 0.6766 (tptt) REVERT: A 390 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 27 outliers final: 10 residues processed: 119 average time/residue: 1.1435 time to fit residues: 144.1523 Evaluate side-chains 104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 154 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 98 ASN R 210 HIS A 236 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.154301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.128132 restraints weight = 14723.112| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.89 r_work: 0.4074 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7022 Z= 0.137 Angle : 0.653 10.508 9543 Z= 0.327 Chirality : 0.044 0.161 1123 Planarity : 0.004 0.058 1189 Dihedral : 5.777 58.208 1023 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.47 % Allowed : 18.19 % Favored : 78.33 % 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: 0.53 (0.29), residues: 869 helix: 1.70 (0.27), residues: 380 sheet: -0.29 (0.37), residues: 193 loop : -0.94 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 326 HIS 0.009 0.001 HIS R 210 PHE 0.018 0.001 PHE A 219 TYR 0.013 0.002 TYR R 176 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 381) hydrogen bonds : angle 4.67329 ( 1113) SS BOND : bond 0.00341 ( 1) SS BOND : angle 1.75604 ( 2) covalent geometry : bond 0.00298 ( 7020) covalent geometry : angle 0.65286 ( 9541) Misc. bond : bond 0.00010 ( 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 127 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.4854 (t80) REVERT: B 269 ILE cc_start: 0.5138 (mm) cc_final: 0.4651 (mt) REVERT: R 115 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7830 (mmpt) REVERT: R 126 SER cc_start: 0.8275 (t) cc_final: 0.8016 (p) REVERT: R 187 LYS cc_start: 0.6882 (mttt) cc_final: 0.6611 (mtpt) REVERT: R 306 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4607 (pp-130) REVERT: R 368 ILE cc_start: 0.8621 (pt) cc_final: 0.8372 (pp) REVERT: A 380 LYS cc_start: 0.7336 (tmtt) cc_final: 0.6922 (ttpt) REVERT: A 390 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8048 (tm-30) outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 0.9796 time to fit residues: 119.0643 Evaluate side-chains 99 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL Chi-restraints excluded: chain B residue 339 TRP 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 147 LEU Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** A 236 GLN A 357 HIS ** 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 = 0.4464 r_free = 0.4464 target = 0.148858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.122242 restraints weight = 14656.449| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.81 r_work: 0.3984 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7022 Z= 0.260 Angle : 0.762 10.662 9543 Z= 0.385 Chirality : 0.048 0.157 1123 Planarity : 0.005 0.056 1189 Dihedral : 6.144 56.662 1023 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 18.75 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 869 helix: 1.43 (0.26), residues: 386 sheet: -0.41 (0.38), residues: 178 loop : -1.09 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.009 0.002 HIS A 362 PHE 0.025 0.002 PHE A 246 TYR 0.048 0.003 TYR R 176 ARG 0.008 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 381) hydrogen bonds : angle 5.04978 ( 1113) SS BOND : bond 0.00995 ( 1) SS BOND : angle 2.30934 ( 2) covalent geometry : bond 0.00594 ( 7020) covalent geometry : angle 0.76179 ( 9541) Misc. bond : bond 0.00029 ( 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 128 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8679 (ptt) cc_final: 0.8260 (ptt) REVERT: B 234 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.4772 (t80) REVERT: B 269 ILE cc_start: 0.5241 (mm) cc_final: 0.4713 (mt) REVERT: P 7 ASP cc_start: 0.6654 (m-30) cc_final: 0.6398 (m-30) REVERT: R 92 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7212 (mp) REVERT: R 130 PHE cc_start: 0.8622 (m-10) cc_final: 0.8147 (m-80) REVERT: R 187 LYS cc_start: 0.6987 (mttt) cc_final: 0.6720 (mtpt) REVERT: R 235 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7151 (mp0) REVERT: R 306 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.4661 (pp-130) REVERT: R 373 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5984 (tmt) REVERT: A 380 LYS cc_start: 0.7343 (tmtt) cc_final: 0.6781 (tptt) REVERT: A 390 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8050 (tm-30) outliers start: 27 outliers final: 13 residues processed: 111 average time/residue: 0.9832 time to fit residues: 116.2458 Evaluate side-chains 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL Chi-restraints excluded: chain G residue 51 LEU 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 306 MET Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.0770 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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** ** 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 = 0.4512 r_free = 0.4512 target = 0.152553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.126811 restraints weight = 14745.736| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.82 r_work: 0.4059 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4104 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= 0.137 Angle : 0.664 8.990 9543 Z= 0.337 Chirality : 0.045 0.188 1123 Planarity : 0.004 0.054 1189 Dihedral : 5.798 56.755 1023 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.89 % Allowed : 19.44 % Favored : 76.67 % 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: 0.49 (0.29), residues: 869 helix: 1.68 (0.27), residues: 384 sheet: -0.33 (0.38), residues: 179 loop : -0.96 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 326 HIS 0.006 0.001 HIS R 210 PHE 0.012 0.001 PHE A 219 TYR 0.021 0.002 TYR R 176 ARG 0.008 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 381) hydrogen bonds : angle 4.70154 ( 1113) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.78257 ( 2) covalent geometry : bond 0.00297 ( 7020) covalent geometry : angle 0.66318 ( 9541) Misc. bond : bond 0.00012 ( 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 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5653 (OUTLIER) cc_final: 0.5014 (t80) REVERT: B 269 ILE cc_start: 0.5036 (mm) cc_final: 0.4601 (mt) REVERT: R 92 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7129 (mp) REVERT: R 126 SER cc_start: 0.8306 (t) cc_final: 0.7929 (p) REVERT: R 205 MET cc_start: 0.3842 (ptp) cc_final: 0.2901 (pmm) REVERT: R 220 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7626 (mm) REVERT: R 235 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7159 (mp0) REVERT: R 306 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4776 (pp-130) REVERT: R 329 ILE cc_start: 0.7958 (tp) cc_final: 0.7639 (mp) REVERT: R 373 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.5918 (tmt) REVERT: A 231 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.5606 (mmm160) REVERT: A 380 LYS cc_start: 0.7316 (tmtt) cc_final: 0.6715 (tptt) REVERT: A 385 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 390 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 28 outliers final: 14 residues processed: 114 average time/residue: 1.0384 time to fit residues: 126.0738 Evaluate side-chains 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER 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 89 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 213 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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** A 236 GLN ** 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 = 0.4538 r_free = 0.4538 target = 0.154505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.128995 restraints weight = 14492.786| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.81 r_work: 0.4091 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7022 Z= 0.128 Angle : 0.671 9.289 9543 Z= 0.337 Chirality : 0.044 0.168 1123 Planarity : 0.004 0.048 1189 Dihedral : 5.621 55.590 1023 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.47 % Allowed : 21.11 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 869 helix: 1.67 (0.27), residues: 382 sheet: -0.55 (0.37), residues: 195 loop : -0.90 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 326 HIS 0.004 0.001 HIS R 210 PHE 0.017 0.001 PHE R 130 TYR 0.037 0.002 TYR R 176 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 381) hydrogen bonds : angle 4.63816 ( 1113) SS BOND : bond 0.00445 ( 1) SS BOND : angle 2.06334 ( 2) covalent geometry : bond 0.00277 ( 7020) covalent geometry : angle 0.66992 ( 9541) Misc. bond : bond 0.00005 ( 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 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 269 ILE cc_start: 0.5124 (mm) cc_final: 0.4691 (mt) REVERT: R 126 SER cc_start: 0.8269 (t) cc_final: 0.7961 (p) REVERT: R 220 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7632 (mm) REVERT: R 235 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7126 (mp0) REVERT: R 306 MET cc_start: 0.5162 (OUTLIER) cc_final: 0.4745 (pp-130) REVERT: R 329 ILE cc_start: 0.7954 (tp) cc_final: 0.7638 (mp) REVERT: R 373 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6019 (tmt) REVERT: A 380 LYS cc_start: 0.7309 (tmtt) cc_final: 0.6722 (tptt) REVERT: A 390 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8019 (tm-30) outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 1.1839 time to fit residues: 143.0033 Evaluate side-chains 106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER 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 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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** A 236 GLN ** 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 = 0.4518 r_free = 0.4518 target = 0.152844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.127088 restraints weight = 14656.232| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.82 r_work: 0.4063 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7022 Z= 0.153 Angle : 0.717 13.165 9543 Z= 0.354 Chirality : 0.044 0.185 1123 Planarity : 0.004 0.045 1189 Dihedral : 5.641 54.343 1023 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.92 % Allowed : 21.94 % Favored : 75.14 % 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: 0.42 (0.29), residues: 869 helix: 1.69 (0.27), residues: 382 sheet: -0.59 (0.37), residues: 188 loop : -0.93 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 326 HIS 0.005 0.001 HIS A 362 PHE 0.020 0.002 PHE R 93 TYR 0.027 0.002 TYR R 176 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 381) hydrogen bonds : angle 4.67442 ( 1113) SS BOND : bond 0.00571 ( 1) SS BOND : angle 2.22624 ( 2) covalent geometry : bond 0.00342 ( 7020) covalent geometry : angle 0.71677 ( 9541) Misc. bond : bond 0.00009 ( 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 113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: B 217 MET cc_start: 0.8561 (ptt) cc_final: 0.8357 (ppp) REVERT: B 234 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.4978 (t80) REVERT: B 269 ILE cc_start: 0.5180 (mm) cc_final: 0.4712 (mt) REVERT: R 126 SER cc_start: 0.8296 (t) cc_final: 0.7824 (p) REVERT: R 205 MET cc_start: 0.3615 (ptp) cc_final: 0.2777 (pmm) REVERT: R 235 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7134 (mp0) REVERT: R 306 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4878 (pp-130) REVERT: R 329 ILE cc_start: 0.7936 (tp) cc_final: 0.7595 (mp) REVERT: R 373 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6068 (tmt) REVERT: R 382 MET cc_start: 0.8719 (ppp) cc_final: 0.8479 (mmt) REVERT: A 380 LYS cc_start: 0.7308 (tmtt) cc_final: 0.6720 (tptt) REVERT: A 390 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8023 (tm-30) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 1.5492 time to fit residues: 171.0438 Evaluate side-chains 103 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 SER 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 89 MET 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 216 ILE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** A 236 GLN ** 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 = 0.4485 r_free = 0.4485 target = 0.149692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.123226 restraints weight = 14870.502| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.81 r_work: 0.4007 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7022 Z= 0.221 Angle : 0.783 12.236 9543 Z= 0.390 Chirality : 0.047 0.242 1123 Planarity : 0.005 0.051 1189 Dihedral : 5.891 54.813 1023 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.89 % Allowed : 21.94 % Favored : 74.17 % 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: 0.14 (0.29), residues: 869 helix: 1.43 (0.26), residues: 383 sheet: -0.67 (0.38), residues: 187 loop : -1.07 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP R 326 HIS 0.005 0.001 HIS R 210 PHE 0.032 0.002 PHE R 93 TYR 0.038 0.002 TYR R 119 ARG 0.006 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 381) hydrogen bonds : angle 4.95548 ( 1113) SS BOND : bond 0.00137 ( 1) SS BOND : angle 2.08345 ( 2) covalent geometry : bond 0.00504 ( 7020) covalent geometry : angle 0.78263 ( 9541) Misc. bond : bond 0.00020 ( 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 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.4925 (t80) REVERT: B 269 ILE cc_start: 0.5151 (mm) cc_final: 0.4728 (mt) REVERT: R 130 PHE cc_start: 0.8562 (m-80) cc_final: 0.8019 (m-80) REVERT: R 235 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7196 (mp0) REVERT: R 306 MET cc_start: 0.5257 (OUTLIER) cc_final: 0.4952 (pp-130) REVERT: R 329 ILE cc_start: 0.8001 (tp) cc_final: 0.7653 (mp) REVERT: R 373 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6086 (tmt) REVERT: R 382 MET cc_start: 0.8725 (ppp) cc_final: 0.8462 (mmt) REVERT: A 231 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5872 (mmm160) REVERT: A 380 LYS cc_start: 0.7316 (tmtt) cc_final: 0.6767 (tptt) REVERT: A 390 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 1.4778 time to fit residues: 163.3483 Evaluate side-chains 105 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER 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 72 MET Chi-restraints excluded: chain R residue 89 MET 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 151 VAL Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 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 = 0.4504 r_free = 0.4504 target = 0.151263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.124959 restraints weight = 14922.965| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.84 r_work: 0.4029 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4608 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 12.480 9543 Z= 0.375 Chirality : 0.046 0.242 1123 Planarity : 0.004 0.047 1189 Dihedral : 5.777 55.329 1023 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.19 % Allowed : 23.06 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.29), residues: 869 helix: 1.51 (0.27), residues: 373 sheet: -0.72 (0.38), residues: 188 loop : -0.99 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 326 HIS 0.008 0.001 HIS R 210 PHE 0.049 0.002 PHE R 93 TYR 0.034 0.002 TYR R 119 ARG 0.005 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 381) hydrogen bonds : angle 4.85670 ( 1113) SS BOND : bond 0.00297 ( 1) SS BOND : angle 1.95284 ( 2) covalent geometry : bond 0.00389 ( 7020) covalent geometry : angle 0.75811 ( 9541) Misc. bond : bond 0.00011 ( 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 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.5135 (t80) REVERT: B 269 ILE cc_start: 0.5281 (mm) cc_final: 0.4795 (mt) REVERT: R 126 SER cc_start: 0.8292 (t) cc_final: 0.7513 (p) REVERT: R 130 PHE cc_start: 0.8520 (m-80) cc_final: 0.8135 (m-80) REVERT: R 235 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7179 (mp0) REVERT: R 306 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4941 (pp-130) REVERT: R 329 ILE cc_start: 0.7944 (tp) cc_final: 0.7602 (mp) REVERT: R 373 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6189 (tmt) REVERT: R 382 MET cc_start: 0.8715 (ppp) cc_final: 0.8448 (mmt) REVERT: A 231 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.5883 (mmm160) REVERT: A 380 LYS cc_start: 0.7311 (tmtt) cc_final: 0.6749 (tptt) REVERT: A 390 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 23 outliers final: 14 residues processed: 101 average time/residue: 1.0449 time to fit residues: 112.5982 Evaluate side-chains 103 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER 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 89 MET 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 220 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN 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 = 0.4504 r_free = 0.4504 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.125104 restraints weight = 14742.250| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.80 r_work: 0.4032 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 7022 Z= 0.265 Angle : 1.094 59.198 9543 Z= 0.632 Chirality : 0.048 0.514 1123 Planarity : 0.005 0.055 1189 Dihedral : 5.898 55.327 1023 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 3.33 % Allowed : 22.64 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 869 helix: 1.53 (0.26), residues: 373 sheet: -0.71 (0.38), residues: 188 loop : -0.96 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 326 HIS 0.008 0.001 HIS R 210 PHE 0.044 0.002 PHE R 93 TYR 0.029 0.002 TYR R 119 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 381) hydrogen bonds : angle 4.86928 ( 1113) SS BOND : bond 0.00312 ( 1) SS BOND : angle 1.86941 ( 2) covalent geometry : bond 0.00514 ( 7020) covalent geometry : angle 1.09421 ( 9541) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7970.92 seconds wall clock time: 139 minutes 24.77 seconds (8364.77 seconds total)