Starting phenix.real_space_refine on Mon Apr 28 12:40:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.map" model { file = "/net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lx5_63466/04_2025/9lx5_63466.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 40 5.16 5 C 4829 2.51 5 N 1293 2.21 5 O 1348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7519 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2452 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2429 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 15, 'TRANS': 308} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2461 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 15, 'TRANS': 313} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.66 Number of scatterers: 7519 At special positions: 0 Unit cell: (85.68, 88.893, 122.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 9 15.00 O 1348 8.00 N 1293 7.00 C 4829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 23.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 28 through 50 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.709A pdb=" N TYR A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.600A pdb=" N ASN A 184 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.241A pdb=" N LYS A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 355 removed outlier: 3.584A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 52 removed outlier: 3.782A pdb=" N GLU B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.922A pdb=" N VAL B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.507A pdb=" N PHE B 185 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.521A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 4.269A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 354 removed outlier: 3.574A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 51 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.969A pdb=" N TYR C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 91' Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 327 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.734A pdb=" N PHE A 311 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 320 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS A 261 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY A 324 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.888A pdb=" N LEU A 307 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 297 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 118 removed outlier: 3.757A pdb=" N GLY A 163 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR A 158 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS A 148 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU A 160 " --> pdb=" O THR A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.505A pdb=" N SER B 64 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.622A pdb=" N THR B 75 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 83 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AB1, first strand: chain 'B' and resid 290 through 298 removed outlier: 3.824A pdb=" N PHE B 297 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 70 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.546A pdb=" N ALA C 73 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 105 removed outlier: 3.574A pdb=" N PHE C 100 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 311 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 254 " --> pdb=" O HIS C 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 112 removed outlier: 3.691A pdb=" N LEU C 307 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 111 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG C 305 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.467A pdb=" N LYS C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 723 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: 1.88 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2423 1.34 - 1.46: 1864 1.46 - 1.58: 3378 1.58 - 1.70: 10 1.70 - 1.82: 49 Bond restraints: 7724 Sorted by residual: bond pdb=" C ARG A 175 " pdb=" N PRO A 176 " ideal model delta sigma weight residual 1.337 1.350 -0.013 9.80e-03 1.04e+04 1.80e+00 bond pdb=" C CYS B 165 " pdb=" N PRO B 166 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" CA PHE B 311 " pdb=" CB PHE B 311 " ideal model delta sigma weight residual 1.525 1.544 -0.019 1.47e-02 4.63e+03 1.68e+00 bond pdb=" CG1 ILE A 193 " pdb=" CD1 ILE A 193 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" C GLY B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.64e-01 ... (remaining 7719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 10259 1.54 - 3.08: 245 3.08 - 4.62: 44 4.62 - 6.16: 9 6.16 - 7.70: 2 Bond angle restraints: 10559 Sorted by residual: angle pdb=" C PHE C 92 " pdb=" N PRO C 93 " pdb=" CA PRO C 93 " ideal model delta sigma weight residual 119.84 115.95 3.89 1.25e+00 6.40e-01 9.71e+00 angle pdb=" C ASN C 153 " pdb=" CA ASN C 153 " pdb=" CB ASN C 153 " ideal model delta sigma weight residual 110.42 115.92 -5.50 1.99e+00 2.53e-01 7.64e+00 angle pdb=" N TYR A 55 " pdb=" CA TYR A 55 " pdb=" CB TYR A 55 " ideal model delta sigma weight residual 113.65 109.89 3.76 1.47e+00 4.63e-01 6.55e+00 angle pdb=" N GLY A 288 " pdb=" CA GLY A 288 " pdb=" C GLY A 288 " ideal model delta sigma weight residual 112.18 115.49 -3.31 1.34e+00 5.57e-01 6.11e+00 angle pdb=" C GLU B 207 " pdb=" N GLU B 208 " pdb=" CA GLU B 208 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.93e+00 ... (remaining 10554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3894 17.12 - 34.24: 534 34.24 - 51.35: 208 51.35 - 68.47: 38 68.47 - 85.59: 12 Dihedral angle restraints: 4686 sinusoidal: 1907 harmonic: 2779 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 165 " pdb=" CB CYS A 165 " ideal model delta sinusoidal sigma weight residual 93.00 176.92 -83.92 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual -86.00 -168.46 82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -134.76 48.76 1 1.00e+01 1.00e-02 3.27e+01 ... (remaining 4683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 723 0.036 - 0.071: 307 0.071 - 0.107: 112 0.107 - 0.143: 36 0.143 - 0.178: 9 Chirality restraints: 1187 Sorted by residual: chirality pdb=" C20 CLR B 401 " pdb=" C17 CLR B 401 " pdb=" C21 CLR B 401 " pdb=" C22 CLR B 401 " both_signs ideal model delta sigma weight residual False 2.59 2.41 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA PHE B 92 " pdb=" N PHE B 92 " pdb=" C PHE B 92 " pdb=" CB PHE B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CB ILE C 45 " pdb=" CA ILE C 45 " pdb=" CG1 ILE C 45 " pdb=" CG2 ILE C 45 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1184 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 81 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 82 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 120 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 121 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 155 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C THR A 155 " -0.025 2.00e-02 2.50e+03 pdb=" O THR A 155 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 156 " 0.008 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1307 2.76 - 3.30: 6807 3.30 - 3.83: 11732 3.83 - 4.37: 12949 4.37 - 4.90: 23614 Nonbonded interactions: 56409 Sorted by model distance: nonbonded pdb=" NE2 GLN B 112 " pdb=" O VAL B 167 " model vdw 2.230 3.120 nonbonded pdb=" O GLY A 250 " pdb=" N PHE A 289 " model vdw 2.250 3.120 nonbonded pdb=" O CYS A 217 " pdb=" NH1 ARG B 139 " model vdw 2.260 3.120 nonbonded pdb=" O THR B 216 " pdb=" OG1 THR B 216 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR C 186 " pdb=" N6 ATP C 401 " model vdw 2.262 2.496 ... (remaining 56404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 31 through 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 166 or \ (resid 167 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 8 through 198 or (resid 199 and (name N or name CA or name C or name O or name C \ B )) or resid 200 through 205 or (resid 206 through 208 and (name N or name CA o \ r name C or name O or name CB )) or resid 209 through 233 or (resid 234 and (nam \ e N or name CA or name C or name O or name CB )) or resid 235 through 245 or (re \ sid 246 through 247 and (name N or name CA or name C or name O or name CB )) or \ resid 248 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 through 274 or (resid 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 345 or (resid \ 346 and (name N or name CA or name C or name O or name CB )) or resid 347 throug \ h 348 or (resid 349 through 354 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'B' and ((resid 31 through 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 128 or \ (resid 129 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 0 through 132 or (resid 133 and (name N or name CA or name C or name O or name C \ B )) or resid 134 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 through 174 or (resid 175 and (name N or n \ ame CA or name C or name O or name CB )) or resid 176 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 23 \ 3 or (resid 234 and (name N or name CA or name C or name O or name CB )) or resi \ d 235 through 245 or (resid 246 through 247 and (name N or name CA or name C or \ name O or name CB )) or resid 248 through 284 or (resid 285 and (name N or name \ CA or name C or name O or name CB )) or resid 286 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 354)) selection = (chain 'C' and ((resid 31 through 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 118 or (resid 119 and (name N or \ name CA or name C or name O or name CB )) or resid 120 through 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 1 \ 32 or (resid 133 and (name N or name CA or name C or name O or name CB )) or res \ id 134 through 159 or (resid 160 and (name N or name CA or name C or name O or n \ ame CB )) or resid 161 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB )) or resid 168 through 174 or (resid 175 and (name N or \ name CA or name C or name O or name CB )) or resid 176 through 198 or (resid 199 \ and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 05 or (resid 206 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 214 or (resid 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 265 or (resid 266 and (name N or name \ CA or name C or name O or name CB )) or resid 267 through 274 or (resid 275 and \ (name N or name CA or name C or name O or name CB )) or resid 276 through 279 o \ r (resid 280 through 283 and (name N or name CA or name C or name O or name CB ) \ ) or resid 284 or (resid 285 and (name N or name CA or name C or name O or name \ CB )) or resid 286 through 345 or (resid 346 and (name N or name CA or name C or \ name O or name CB )) or resid 347 through 354)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.160 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.004 0.044 7741 Z= 0.155 Angle : 0.590 7.697 10589 Z= 0.316 Chirality : 0.048 0.178 1187 Planarity : 0.004 0.043 1336 Dihedral : 17.832 85.590 2863 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.22 % Allowed : 36.05 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.29), residues: 975 helix: 2.70 (0.40), residues: 187 sheet: -0.61 (0.34), residues: 288 loop : -2.87 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 259 HIS 0.007 0.001 HIS B 120 PHE 0.014 0.002 PHE A 195 TYR 0.010 0.001 TYR A 90 ARG 0.003 0.000 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.13892 ( 265) hydrogen bonds : angle 5.93580 ( 723) SS BOND : bond 0.00371 ( 15) SS BOND : angle 1.15367 ( 30) covalent geometry : bond 0.00351 ( 7724) covalent geometry : angle 0.58784 (10559) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.864 Fit side-chains REVERT: A 97 ASP cc_start: 0.8839 (t0) cc_final: 0.8566 (t0) REVERT: B 52 GLU cc_start: 0.8338 (pt0) cc_final: 0.7717 (pm20) REVERT: B 193 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7394 (mp) REVERT: B 279 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7259 (tt) REVERT: B 322 LYS cc_start: 0.7391 (mmmm) cc_final: 0.6070 (pttt) REVERT: C 172 ASP cc_start: 0.8091 (m-30) cc_final: 0.7027 (p0) REVERT: C 216 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7906 (t) REVERT: C 265 TRP cc_start: 0.8808 (m-10) cc_final: 0.8306 (m-10) REVERT: C 280 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4686 (m-80) outliers start: 31 outliers final: 23 residues processed: 110 average time/residue: 0.1548 time to fit residues: 24.8619 Evaluate side-chains 110 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN C 76 GLN C 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122484 restraints weight = 9292.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124026 restraints weight = 7304.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125552 restraints weight = 6257.012| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7741 Z= 0.121 Angle : 0.547 5.911 10589 Z= 0.291 Chirality : 0.047 0.178 1187 Planarity : 0.004 0.045 1336 Dihedral : 10.189 71.357 1382 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 8.44 % Allowed : 31.29 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 975 helix: 2.64 (0.40), residues: 188 sheet: -0.69 (0.35), residues: 267 loop : -2.85 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.003 0.001 HIS B 120 PHE 0.013 0.001 PHE A 92 TYR 0.017 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 265) hydrogen bonds : angle 4.84910 ( 723) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.75974 ( 30) covalent geometry : bond 0.00272 ( 7724) covalent geometry : angle 0.54674 (10559) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 95 time to evaluate : 0.755 Fit side-chains REVERT: A 97 ASP cc_start: 0.8827 (t0) cc_final: 0.8453 (t0) REVERT: A 180 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6196 (ptp90) REVERT: B 52 GLU cc_start: 0.8294 (pt0) cc_final: 0.7628 (pm20) REVERT: B 184 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7663 (m110) REVERT: B 193 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7604 (mp) REVERT: B 213 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6379 (t-170) REVERT: B 309 LYS cc_start: 0.8747 (tttt) cc_final: 0.8314 (tttp) REVERT: B 322 LYS cc_start: 0.7130 (mmmm) cc_final: 0.5794 (pttt) REVERT: C 69 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 129 ASP cc_start: 0.8512 (t0) cc_final: 0.8187 (t70) REVERT: C 172 ASP cc_start: 0.8117 (m-30) cc_final: 0.7046 (p0) REVERT: C 216 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7626 (t) REVERT: C 265 TRP cc_start: 0.8806 (m-10) cc_final: 0.8323 (m-10) REVERT: C 280 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.4696 (m-80) outliers start: 62 outliers final: 35 residues processed: 144 average time/residue: 0.1391 time to fit residues: 29.4573 Evaluate side-chains 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 chunk 64 optimal weight: 70.0000 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.161690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123071 restraints weight = 9469.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124816 restraints weight = 7373.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126157 restraints weight = 6255.696| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7741 Z= 0.124 Angle : 0.543 6.010 10589 Z= 0.288 Chirality : 0.047 0.179 1187 Planarity : 0.004 0.044 1336 Dihedral : 10.065 71.351 1375 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 8.84 % Allowed : 30.88 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.29), residues: 975 helix: 2.75 (0.40), residues: 188 sheet: -0.75 (0.33), residues: 289 loop : -2.79 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.003 0.000 HIS A 277 PHE 0.014 0.001 PHE A 92 TYR 0.015 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02519 ( 265) hydrogen bonds : angle 4.53810 ( 723) SS BOND : bond 0.00292 ( 15) SS BOND : angle 0.85114 ( 30) covalent geometry : bond 0.00285 ( 7724) covalent geometry : angle 0.54209 (10559) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 91 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8829 (t0) cc_final: 0.8585 (t0) REVERT: A 136 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7551 (mtpp) REVERT: B 52 GLU cc_start: 0.8272 (pt0) cc_final: 0.7602 (pm20) REVERT: B 184 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7669 (m110) REVERT: B 279 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7089 (tt) REVERT: B 322 LYS cc_start: 0.7302 (mmmm) cc_final: 0.5990 (pttt) REVERT: C 69 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 103 MET cc_start: 0.8271 (ttp) cc_final: 0.8004 (ttm) REVERT: C 172 ASP cc_start: 0.8137 (m-30) cc_final: 0.7033 (p0) REVERT: C 216 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7625 (t) REVERT: C 265 TRP cc_start: 0.8791 (m-10) cc_final: 0.8322 (m-10) REVERT: C 280 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4727 (m-80) outliers start: 65 outliers final: 40 residues processed: 144 average time/residue: 0.1264 time to fit residues: 27.6459 Evaluate side-chains 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121017 restraints weight = 9438.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120821 restraints weight = 7558.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123299 restraints weight = 7139.019| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7741 Z= 0.147 Angle : 0.560 6.050 10589 Z= 0.297 Chirality : 0.048 0.181 1187 Planarity : 0.004 0.044 1336 Dihedral : 10.121 72.246 1371 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 8.98 % Allowed : 30.07 % Favored : 60.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.29), residues: 975 helix: 2.78 (0.40), residues: 188 sheet: -0.71 (0.33), residues: 288 loop : -2.81 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.009 0.001 HIS B 269 PHE 0.015 0.001 PHE A 92 TYR 0.014 0.001 TYR B 90 ARG 0.002 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.02491 ( 265) hydrogen bonds : angle 4.48306 ( 723) SS BOND : bond 0.00316 ( 15) SS BOND : angle 0.87150 ( 30) covalent geometry : bond 0.00343 ( 7724) covalent geometry : angle 0.55874 (10559) Misc. bond : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 86 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7580 (mtpp) REVERT: B 52 GLU cc_start: 0.8281 (pt0) cc_final: 0.7648 (pm20) REVERT: B 279 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7177 (tt) REVERT: B 322 LYS cc_start: 0.7410 (mmmm) cc_final: 0.6178 (pttt) REVERT: C 47 TRP cc_start: 0.6987 (OUTLIER) cc_final: 0.6649 (t-100) REVERT: C 69 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 103 MET cc_start: 0.8299 (ttp) cc_final: 0.8052 (ttm) REVERT: C 129 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8148 (t70) REVERT: C 172 ASP cc_start: 0.8124 (m-30) cc_final: 0.7007 (p0) REVERT: C 216 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7519 (t) REVERT: C 265 TRP cc_start: 0.8794 (m-10) cc_final: 0.8297 (m-10) REVERT: C 280 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4753 (m-80) outliers start: 66 outliers final: 42 residues processed: 142 average time/residue: 0.1452 time to fit residues: 30.1122 Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 82 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 184 ASN B 269 HIS C 76 GLN C 277 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118687 restraints weight = 9401.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116438 restraints weight = 8933.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118176 restraints weight = 7947.051| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7741 Z= 0.200 Angle : 0.622 6.349 10589 Z= 0.328 Chirality : 0.051 0.227 1187 Planarity : 0.004 0.045 1336 Dihedral : 10.493 74.149 1371 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 9.12 % Allowed : 29.80 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.29), residues: 975 helix: 1.89 (0.39), residues: 212 sheet: -0.79 (0.34), residues: 281 loop : -2.89 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 85 HIS 0.006 0.001 HIS B 120 PHE 0.016 0.002 PHE B 311 TYR 0.015 0.001 TYR A 55 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.02676 ( 265) hydrogen bonds : angle 4.53118 ( 723) SS BOND : bond 0.00395 ( 15) SS BOND : angle 1.01339 ( 30) covalent geometry : bond 0.00480 ( 7724) covalent geometry : angle 0.62082 (10559) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 83 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7612 (mtpp) REVERT: B 52 GLU cc_start: 0.8271 (pt0) cc_final: 0.7665 (pm20) REVERT: B 213 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6662 (t-170) REVERT: B 279 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B 322 LYS cc_start: 0.7617 (mmmm) cc_final: 0.6381 (pttt) REVERT: C 47 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6815 (t-100) REVERT: C 69 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 129 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8260 (t70) REVERT: C 172 ASP cc_start: 0.8157 (m-30) cc_final: 0.6984 (p0) REVERT: C 216 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7647 (t) REVERT: C 265 TRP cc_start: 0.8778 (m-10) cc_final: 0.8461 (m-10) REVERT: C 280 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: C 305 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8971 (ptt180) outliers start: 67 outliers final: 42 residues processed: 138 average time/residue: 0.1478 time to fit residues: 30.1289 Evaluate side-chains 135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116914 restraints weight = 9428.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119337 restraints weight = 6755.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120826 restraints weight = 5440.228| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7741 Z= 0.135 Angle : 0.582 11.518 10589 Z= 0.303 Chirality : 0.048 0.183 1187 Planarity : 0.004 0.046 1336 Dihedral : 10.391 75.043 1371 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 8.16 % Allowed : 30.48 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.29), residues: 975 helix: 2.12 (0.39), residues: 206 sheet: -0.81 (0.33), residues: 288 loop : -2.87 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 85 HIS 0.004 0.000 HIS A 277 PHE 0.020 0.001 PHE A 92 TYR 0.017 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02396 ( 265) hydrogen bonds : angle 4.40895 ( 723) SS BOND : bond 0.00303 ( 15) SS BOND : angle 0.88453 ( 30) covalent geometry : bond 0.00315 ( 7724) covalent geometry : angle 0.58108 (10559) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 85 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7576 (mtpp) REVERT: B 52 GLU cc_start: 0.8221 (pt0) cc_final: 0.7675 (pm20) REVERT: B 279 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7283 (tt) REVERT: B 309 LYS cc_start: 0.8837 (tttt) cc_final: 0.8537 (tttp) REVERT: B 322 LYS cc_start: 0.7533 (mmmm) cc_final: 0.6310 (pttt) REVERT: C 47 TRP cc_start: 0.7211 (OUTLIER) cc_final: 0.6862 (t-100) REVERT: C 69 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 103 MET cc_start: 0.8291 (ttp) cc_final: 0.8047 (ttm) REVERT: C 172 ASP cc_start: 0.8097 (m-30) cc_final: 0.6976 (p0) REVERT: C 216 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7565 (t) REVERT: C 265 TRP cc_start: 0.8774 (m-10) cc_final: 0.8269 (m-10) REVERT: C 280 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.4798 (m-80) REVERT: C 305 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.9024 (ptt180) outliers start: 60 outliers final: 47 residues processed: 135 average time/residue: 0.1407 time to fit residues: 28.1426 Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 79 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118881 restraints weight = 9305.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121081 restraints weight = 6929.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122341 restraints weight = 5717.655| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7741 Z= 0.130 Angle : 0.576 12.911 10589 Z= 0.300 Chirality : 0.048 0.194 1187 Planarity : 0.004 0.045 1336 Dihedral : 10.328 75.434 1371 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 8.71 % Allowed : 29.80 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.29), residues: 975 helix: 2.13 (0.39), residues: 206 sheet: -0.75 (0.33), residues: 288 loop : -2.84 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.003 0.000 HIS A 277 PHE 0.027 0.001 PHE C 152 TYR 0.017 0.001 TYR B 90 ARG 0.002 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.02325 ( 265) hydrogen bonds : angle 4.33960 ( 723) SS BOND : bond 0.00305 ( 15) SS BOND : angle 0.86274 ( 30) covalent geometry : bond 0.00302 ( 7724) covalent geometry : angle 0.57529 (10559) Misc. bond : bond 0.00131 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 88 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7503 (mtpp) REVERT: B 52 GLU cc_start: 0.8244 (pt0) cc_final: 0.7652 (pm20) REVERT: B 213 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6594 (t-170) REVERT: B 279 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7146 (tt) REVERT: B 309 LYS cc_start: 0.8810 (tttt) cc_final: 0.8503 (tttp) REVERT: B 322 LYS cc_start: 0.7438 (mmmm) cc_final: 0.6190 (pttt) REVERT: C 47 TRP cc_start: 0.7122 (OUTLIER) cc_final: 0.6784 (t-100) REVERT: C 69 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (mp) REVERT: C 172 ASP cc_start: 0.8134 (m-30) cc_final: 0.6941 (p0) REVERT: C 216 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7561 (t) REVERT: C 265 TRP cc_start: 0.8795 (m-10) cc_final: 0.8302 (m-10) REVERT: C 280 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: C 305 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8981 (ptt180) outliers start: 64 outliers final: 48 residues processed: 141 average time/residue: 0.1444 time to fit residues: 30.0097 Evaluate side-chains 139 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 83 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.155508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118593 restraints weight = 9516.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117404 restraints weight = 8312.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118478 restraints weight = 7407.065| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7741 Z= 0.182 Angle : 0.617 11.408 10589 Z= 0.325 Chirality : 0.050 0.235 1187 Planarity : 0.004 0.047 1336 Dihedral : 10.591 76.631 1371 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 8.71 % Allowed : 29.66 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.29), residues: 975 helix: 1.88 (0.39), residues: 212 sheet: -0.87 (0.33), residues: 289 loop : -2.90 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 85 HIS 0.010 0.001 HIS B 120 PHE 0.027 0.002 PHE C 152 TYR 0.014 0.001 TYR A 55 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 265) hydrogen bonds : angle 4.41612 ( 723) SS BOND : bond 0.00379 ( 15) SS BOND : angle 0.97760 ( 30) covalent geometry : bond 0.00434 ( 7724) covalent geometry : angle 0.61591 (10559) Misc. bond : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 85 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7550 (mtpp) REVERT: B 52 GLU cc_start: 0.8235 (pt0) cc_final: 0.7618 (pm20) REVERT: B 213 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.6589 (t-170) REVERT: B 279 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7211 (tt) REVERT: B 309 LYS cc_start: 0.8883 (tttt) cc_final: 0.8571 (tttp) REVERT: B 322 LYS cc_start: 0.7581 (mmmm) cc_final: 0.6349 (pttt) REVERT: C 47 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6903 (t-100) REVERT: C 69 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 129 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8238 (t70) REVERT: C 150 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (m) REVERT: C 172 ASP cc_start: 0.8156 (m-30) cc_final: 0.6946 (p0) REVERT: C 216 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7604 (t) REVERT: C 265 TRP cc_start: 0.8787 (m-10) cc_final: 0.8255 (m-10) REVERT: C 280 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.4878 (m-80) REVERT: C 305 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8990 (ptt180) outliers start: 64 outliers final: 47 residues processed: 136 average time/residue: 0.1483 time to fit residues: 29.7199 Evaluate side-chains 140 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 83 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118703 restraints weight = 9564.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116470 restraints weight = 8532.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118303 restraints weight = 7826.564| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7741 Z= 0.156 Angle : 0.602 11.040 10589 Z= 0.316 Chirality : 0.049 0.208 1187 Planarity : 0.004 0.047 1336 Dihedral : 10.538 77.718 1371 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 8.71 % Allowed : 29.93 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.28), residues: 975 helix: 1.89 (0.39), residues: 212 sheet: -0.86 (0.33), residues: 288 loop : -2.89 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 85 HIS 0.011 0.001 HIS B 120 PHE 0.029 0.002 PHE C 152 TYR 0.016 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02448 ( 265) hydrogen bonds : angle 4.40936 ( 723) SS BOND : bond 0.00354 ( 15) SS BOND : angle 1.04436 ( 30) covalent geometry : bond 0.00370 ( 7724) covalent geometry : angle 0.60044 (10559) Misc. bond : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 77 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7527 (mtpp) REVERT: B 52 GLU cc_start: 0.8269 (pt0) cc_final: 0.7609 (pm20) REVERT: B 213 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6552 (t-170) REVERT: B 279 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B 309 LYS cc_start: 0.8879 (tttt) cc_final: 0.8577 (tttp) REVERT: B 322 LYS cc_start: 0.7546 (mmmm) cc_final: 0.6362 (pttt) REVERT: C 47 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.6916 (t-100) REVERT: C 69 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8311 (mp) REVERT: C 129 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8230 (t70) REVERT: C 150 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (m) REVERT: C 216 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7542 (t) REVERT: C 265 TRP cc_start: 0.8781 (m-10) cc_final: 0.8249 (m-10) REVERT: C 280 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: C 305 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.9070 (ptt180) outliers start: 64 outliers final: 48 residues processed: 128 average time/residue: 0.1448 time to fit residues: 27.3878 Evaluate side-chains 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 74 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123269 restraints weight = 9439.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120897 restraints weight = 10669.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122882 restraints weight = 9977.505| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7741 Z= 0.160 Angle : 0.606 10.389 10589 Z= 0.318 Chirality : 0.050 0.209 1187 Planarity : 0.004 0.047 1336 Dihedral : 10.469 78.271 1369 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 8.30 % Allowed : 30.48 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.28), residues: 975 helix: 1.79 (0.39), residues: 213 sheet: -0.87 (0.33), residues: 288 loop : -2.92 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 85 HIS 0.011 0.001 HIS B 120 PHE 0.034 0.002 PHE C 152 TYR 0.015 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02486 ( 265) hydrogen bonds : angle 4.41602 ( 723) SS BOND : bond 0.00344 ( 15) SS BOND : angle 1.10121 ( 30) covalent geometry : bond 0.00379 ( 7724) covalent geometry : angle 0.60379 (10559) Misc. bond : bond 0.00144 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 77 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: B 52 GLU cc_start: 0.8136 (pt0) cc_final: 0.7609 (pm20) REVERT: B 213 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6541 (t-170) REVERT: B 279 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7159 (tt) REVERT: B 309 LYS cc_start: 0.8850 (tttt) cc_final: 0.8567 (tttp) REVERT: B 322 LYS cc_start: 0.7589 (mmmm) cc_final: 0.6396 (pttt) REVERT: C 47 TRP cc_start: 0.7415 (OUTLIER) cc_final: 0.7116 (t-100) REVERT: C 69 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8256 (mp) REVERT: C 129 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8205 (t70) REVERT: C 150 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8690 (m) REVERT: C 216 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7490 (t) REVERT: C 265 TRP cc_start: 0.8768 (m-10) cc_final: 0.8270 (m-10) REVERT: C 280 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: C 305 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.8974 (ptt180) outliers start: 61 outliers final: 48 residues processed: 127 average time/residue: 0.1435 time to fit residues: 26.9154 Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 75 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 47 TRP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118243 restraints weight = 9432.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120302 restraints weight = 7177.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121461 restraints weight = 5989.562| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7741 Z= 0.139 Angle : 0.588 9.778 10589 Z= 0.309 Chirality : 0.049 0.182 1187 Planarity : 0.004 0.047 1336 Dihedral : 10.382 77.467 1369 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 8.03 % Allowed : 30.61 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.28), residues: 975 helix: 2.01 (0.39), residues: 207 sheet: -0.83 (0.33), residues: 288 loop : -2.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.010 0.001 HIS B 120 PHE 0.035 0.002 PHE C 152 TYR 0.016 0.001 TYR B 90 ARG 0.002 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.02399 ( 265) hydrogen bonds : angle 4.38383 ( 723) SS BOND : bond 0.00325 ( 15) SS BOND : angle 0.99306 ( 30) covalent geometry : bond 0.00326 ( 7724) covalent geometry : angle 0.58659 (10559) Misc. bond : bond 0.00133 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.91 seconds wall clock time: 44 minutes 16.69 seconds (2656.69 seconds total)