Starting phenix.real_space_refine on Sun May 11 00:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/05_2025/8h8d_34543.cif" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4587 2.51 5 N 1179 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7054 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2366 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2337 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "C" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2351 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Time building chain proxies: 4.86, per 1000 atoms: 0.69 Number of scatterers: 7054 At special positions: 0 Unit cell: (80.438, 80.438, 140.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1249 8.00 N 1179 7.00 C 4587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 151 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 957.4 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 34.5% alpha, 28.7% 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 56 through 99 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.655A pdb=" N PHE A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 304 through 343 Processing helix chain 'B' and resid 61 through 97 removed outlier: 3.689A pdb=" N MET B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.716A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 304 through 342 removed outlier: 3.789A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 99 removed outlier: 4.051A pdb=" N TYR C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.521A pdb=" N CYS C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 344 removed outlier: 3.575A pdb=" N ALA C 310 " --> pdb=" O TRP C 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.944A pdb=" N GLN A 295 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 299 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS A 190 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU A 126 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.944A pdb=" N GLN A 295 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 299 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 261 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.716A pdb=" N ILE A 172 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 201 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 108 removed outlier: 8.167A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 159 removed outlier: 3.506A pdb=" N GLN B 154 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 156 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 170 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 117 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 202 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 131 removed outlier: 3.640A pdb=" N HIS B 190 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN B 188 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 129 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 186 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE B 238 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 284 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 108 removed outlier: 14.129A pdb=" N TYR C 293 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N MET C 244 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLN C 295 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 240 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 188 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 128 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS C 190 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU C 126 " --> pdb=" O HIS C 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 108 removed outlier: 14.129A pdb=" N TYR C 293 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N MET C 244 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLN C 295 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 243 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 120 removed outlier: 4.371A pdb=" N ASP C 202 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159 374 hydrogen bonds defined for protein. 1062 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: 1.99 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1833 1.33 - 1.45: 1377 1.45 - 1.57: 3970 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 7243 Sorted by residual: bond pdb=" CE1 HIS B 340 " pdb=" NE2 HIS B 340 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.60e+01 bond pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL B 330 " pdb=" CA VAL B 330 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.87e+00 bond pdb=" N ILE B 301 " pdb=" CA ILE B 301 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.72e+00 bond pdb=" N ILE A 301 " pdb=" CA ILE A 301 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.71e+00 ... (remaining 7238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9436 2.16 - 4.31: 310 4.31 - 6.47: 32 6.47 - 8.62: 9 8.62 - 10.78: 6 Bond angle restraints: 9793 Sorted by residual: angle pdb=" C ILE A 159 " pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta sigma weight residual 120.49 131.27 -10.78 1.42e+00 4.96e-01 5.76e+01 angle pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" C LYS A 321 " ideal model delta sigma weight residual 111.36 105.92 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" CA ARG B 182 " pdb=" CB ARG B 182 " pdb=" CG ARG B 182 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 111.28 115.55 -4.27 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 109.07 115.28 -6.21 1.61e+00 3.86e-01 1.49e+01 ... (remaining 9788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3622 17.90 - 35.81: 530 35.81 - 53.71: 137 53.71 - 71.62: 30 71.62 - 89.52: 13 Dihedral angle restraints: 4332 sinusoidal: 1795 harmonic: 2537 Sorted by residual: dihedral pdb=" CD ARG B 337 " pdb=" NE ARG B 337 " pdb=" CZ ARG B 337 " pdb=" NH1 ARG B 337 " ideal model delta sinusoidal sigma weight residual 0.00 -78.44 78.44 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS B 129 " pdb=" SG CYS B 129 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual 93.00 41.68 51.32 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" CD ARG B 339 " pdb=" NE ARG B 339 " pdb=" CZ ARG B 339 " pdb=" NH1 ARG B 339 " ideal model delta sinusoidal sigma weight residual 0.00 -48.39 48.39 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 765 0.044 - 0.089: 192 0.089 - 0.133: 76 0.133 - 0.178: 14 0.178 - 0.222: 17 Chirality restraints: 1064 Sorted by residual: chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL B 318 " pdb=" CA VAL B 318 " pdb=" CG1 VAL B 318 " pdb=" CG2 VAL B 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1061 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 337 " 1.083 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 337 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B 337 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 337 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 337 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 339 " 0.820 9.50e-02 1.11e+02 3.67e-01 8.20e+01 pdb=" NE ARG B 339 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 339 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 339 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 339 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 197 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" CG ASP A 197 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 197 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 197 " 0.017 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 271 2.70 - 3.25: 7641 3.25 - 3.80: 11911 3.80 - 4.35: 14178 4.35 - 4.90: 21981 Nonbonded interactions: 55982 Sorted by model distance: nonbonded pdb=" OD1 ASP A 197 " pdb=" N PHE A 198 " model vdw 2.155 3.120 nonbonded pdb=" O ARG B 181 " pdb=" NH1 ARG B 181 " model vdw 2.192 3.120 nonbonded pdb=" O ALA B 211 " pdb=" OG SER B 215 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 302 " pdb=" OD1 ASN C 304 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN B 268 " pdb=" N PHE B 269 " model vdw 2.232 3.120 ... (remaining 55977 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 61 through 342) selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) } 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: 0.010 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.020 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 0.040 7246 Z= 0.282 Angle : 0.868 10.779 9799 Z= 0.539 Chirality : 0.053 0.222 1064 Planarity : 0.018 0.485 1229 Dihedral : 18.367 89.523 2671 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.97 % Allowed : 30.45 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 850 helix: 1.85 (0.30), residues: 288 sheet: -0.45 (0.31), residues: 289 loop : -1.49 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 133 HIS 0.007 0.001 HIS C 132 PHE 0.022 0.001 PHE A 320 TYR 0.014 0.001 TYR A 120 ARG 0.003 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.20476 ( 357) hydrogen bonds : angle 7.40718 ( 1062) SS BOND : bond 0.00138 ( 3) SS BOND : angle 1.81238 ( 6) covalent geometry : bond 0.00444 ( 7243) covalent geometry : angle 0.86688 ( 9793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8608 (ptm) cc_final: 0.8395 (ppp) REVERT: B 325 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9100 (p90) REVERT: B 338 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4702 (mmm160) REVERT: B 340 HIS cc_start: -0.2636 (OUTLIER) cc_final: -0.2867 (t-90) REVERT: C 154 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 39 outliers final: 17 residues processed: 130 average time/residue: 0.1949 time to fit residues: 33.4530 Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.091847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065461 restraints weight = 26591.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067050 restraints weight = 16630.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068153 restraints weight = 12412.809| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7246 Z= 0.185 Angle : 0.659 8.383 9799 Z= 0.347 Chirality : 0.044 0.184 1064 Planarity : 0.005 0.087 1229 Dihedral : 4.878 20.204 928 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 850 helix: 1.34 (0.29), residues: 293 sheet: -0.43 (0.31), residues: 295 loop : -1.45 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 232 HIS 0.006 0.001 HIS C 190 PHE 0.024 0.002 PHE A 320 TYR 0.017 0.002 TYR B 158 ARG 0.020 0.001 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 357) hydrogen bonds : angle 5.45644 ( 1062) SS BOND : bond 0.00400 ( 3) SS BOND : angle 2.09864 ( 6) covalent geometry : bond 0.00410 ( 7243) covalent geometry : angle 0.65743 ( 9793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8737 (ptm) cc_final: 0.8475 (ppp) REVERT: B 158 TYR cc_start: 0.8080 (m-10) cc_final: 0.7873 (m-10) REVERT: B 333 MET cc_start: 0.6801 (tpp) cc_final: 0.6308 (tmm) REVERT: C 79 MET cc_start: 0.8811 (mmp) cc_final: 0.8520 (mmm) REVERT: C 169 HIS cc_start: 0.7768 (t-170) cc_final: 0.7550 (t-90) REVERT: C 222 MET cc_start: 0.8589 (ppp) cc_final: 0.8352 (ppp) REVERT: C 233 LYS cc_start: 0.9030 (tptt) cc_final: 0.8771 (tptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1682 time to fit residues: 31.3025 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 55 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 174 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069975 restraints weight = 26929.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.070421 restraints weight = 19647.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070706 restraints weight = 14393.105| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7246 Z= 0.121 Angle : 0.608 7.250 9799 Z= 0.312 Chirality : 0.042 0.148 1064 Planarity : 0.004 0.074 1229 Dihedral : 4.658 20.844 928 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.30), residues: 850 helix: 1.28 (0.29), residues: 293 sheet: -0.32 (0.30), residues: 293 loop : -1.41 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.004 0.001 HIS B 136 PHE 0.018 0.001 PHE C 325 TYR 0.015 0.001 TYR B 158 ARG 0.005 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 357) hydrogen bonds : angle 4.86752 ( 1062) SS BOND : bond 0.00123 ( 3) SS BOND : angle 1.00102 ( 6) covalent geometry : bond 0.00262 ( 7243) covalent geometry : angle 0.60721 ( 9793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9103 (tmm) cc_final: 0.8860 (tmm) REVERT: B 222 MET cc_start: 0.7919 (tmm) cc_final: 0.7617 (tmm) REVERT: B 309 ILE cc_start: 0.9573 (tp) cc_final: 0.9350 (pt) REVERT: B 333 MET cc_start: 0.7028 (tpp) cc_final: 0.6457 (tmm) REVERT: C 79 MET cc_start: 0.8914 (mmp) cc_final: 0.8469 (mmm) REVERT: C 222 MET cc_start: 0.8556 (ppp) cc_final: 0.8350 (ppp) REVERT: C 321 LYS cc_start: 0.9641 (tttm) cc_final: 0.9420 (tppt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1746 time to fit residues: 28.8400 Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.068562 restraints weight = 27389.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069029 restraints weight = 20290.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.069407 restraints weight = 14657.602| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7246 Z= 0.139 Angle : 0.587 8.999 9799 Z= 0.303 Chirality : 0.041 0.170 1064 Planarity : 0.005 0.116 1229 Dihedral : 4.618 19.911 928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 850 helix: 1.41 (0.28), residues: 290 sheet: -0.28 (0.31), residues: 296 loop : -1.48 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 232 HIS 0.011 0.001 HIS C 132 PHE 0.013 0.001 PHE A 320 TYR 0.017 0.001 TYR C 203 ARG 0.025 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 357) hydrogen bonds : angle 4.67440 ( 1062) SS BOND : bond 0.00769 ( 3) SS BOND : angle 1.63782 ( 6) covalent geometry : bond 0.00307 ( 7243) covalent geometry : angle 0.58543 ( 9793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9163 (tmm) cc_final: 0.8880 (tmm) REVERT: B 222 MET cc_start: 0.7904 (tmm) cc_final: 0.7670 (tmm) REVERT: B 309 ILE cc_start: 0.9515 (tp) cc_final: 0.9281 (pt) REVERT: B 333 MET cc_start: 0.6968 (tpp) cc_final: 0.6501 (tmm) REVERT: C 79 MET cc_start: 0.8857 (mmp) cc_final: 0.8428 (mmm) REVERT: C 222 MET cc_start: 0.8561 (ppp) cc_final: 0.8318 (ppp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1604 time to fit residues: 26.6288 Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 35 optimal weight: 0.0970 chunk 57 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.091935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068720 restraints weight = 26362.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069132 restraints weight = 18993.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069498 restraints weight = 14058.282| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7246 Z= 0.132 Angle : 0.591 7.564 9799 Z= 0.305 Chirality : 0.041 0.160 1064 Planarity : 0.005 0.118 1229 Dihedral : 4.566 20.543 928 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.30), residues: 850 helix: 1.53 (0.29), residues: 288 sheet: -0.19 (0.31), residues: 286 loop : -1.35 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 232 HIS 0.011 0.001 HIS C 132 PHE 0.021 0.001 PHE B 316 TYR 0.018 0.001 TYR C 203 ARG 0.012 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 357) hydrogen bonds : angle 4.56063 ( 1062) SS BOND : bond 0.00096 ( 3) SS BOND : angle 1.24407 ( 6) covalent geometry : bond 0.00292 ( 7243) covalent geometry : angle 0.59066 ( 9793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9211 (tmm) cc_final: 0.8938 (tmm) REVERT: B 333 MET cc_start: 0.7033 (tpp) cc_final: 0.6598 (tmm) REVERT: C 79 MET cc_start: 0.8854 (mmp) cc_final: 0.8399 (mmm) REVERT: C 222 MET cc_start: 0.8606 (ppp) cc_final: 0.8350 (ppp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1599 time to fit residues: 25.7987 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN C 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064428 restraints weight = 27067.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066081 restraints weight = 16673.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067207 restraints weight = 12250.376| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7246 Z= 0.144 Angle : 0.590 7.442 9799 Z= 0.304 Chirality : 0.041 0.150 1064 Planarity : 0.005 0.107 1229 Dihedral : 4.614 19.468 928 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 850 helix: 1.59 (0.29), residues: 288 sheet: -0.20 (0.31), residues: 292 loop : -1.41 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 232 HIS 0.013 0.001 HIS C 132 PHE 0.020 0.001 PHE A 316 TYR 0.020 0.001 TYR C 203 ARG 0.010 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 357) hydrogen bonds : angle 4.56876 ( 1062) SS BOND : bond 0.00127 ( 3) SS BOND : angle 1.35845 ( 6) covalent geometry : bond 0.00324 ( 7243) covalent geometry : angle 0.58926 ( 9793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9174 (tmm) cc_final: 0.8921 (tmm) REVERT: A 316 PHE cc_start: 0.9398 (m-80) cc_final: 0.9156 (m-80) REVERT: B 222 MET cc_start: 0.7918 (tmm) cc_final: 0.7683 (tmm) REVERT: B 333 MET cc_start: 0.6868 (tpp) cc_final: 0.6466 (tmm) REVERT: C 79 MET cc_start: 0.8873 (mmp) cc_final: 0.8458 (mmm) REVERT: C 222 MET cc_start: 0.8628 (ppp) cc_final: 0.8338 (ppp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1592 time to fit residues: 24.6320 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 0.0010 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.092993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069503 restraints weight = 26856.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070019 restraints weight = 19504.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070292 restraints weight = 14640.683| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7246 Z= 0.107 Angle : 0.603 8.273 9799 Z= 0.302 Chirality : 0.043 0.257 1064 Planarity : 0.004 0.094 1229 Dihedral : 4.454 20.616 928 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 850 helix: 1.54 (0.29), residues: 289 sheet: -0.10 (0.31), residues: 286 loop : -1.31 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 289 HIS 0.010 0.001 HIS C 132 PHE 0.022 0.001 PHE B 316 TYR 0.016 0.001 TYR C 203 ARG 0.007 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 357) hydrogen bonds : angle 4.35819 ( 1062) SS BOND : bond 0.00329 ( 3) SS BOND : angle 1.34476 ( 6) covalent geometry : bond 0.00236 ( 7243) covalent geometry : angle 0.60250 ( 9793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9177 (tmm) cc_final: 0.8880 (tmm) REVERT: B 333 MET cc_start: 0.7164 (tpp) cc_final: 0.6670 (tmm) REVERT: C 79 MET cc_start: 0.8859 (mmp) cc_final: 0.8465 (mmm) REVERT: C 222 MET cc_start: 0.8651 (ppp) cc_final: 0.8362 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1672 time to fit residues: 26.7455 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.092109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065969 restraints weight = 26995.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067666 restraints weight = 16672.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068809 restraints weight = 12189.600| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7246 Z= 0.116 Angle : 0.612 7.583 9799 Z= 0.305 Chirality : 0.042 0.228 1064 Planarity : 0.004 0.085 1229 Dihedral : 4.397 19.822 928 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 850 helix: 1.51 (0.29), residues: 289 sheet: -0.10 (0.31), residues: 292 loop : -1.30 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 PHE 0.018 0.001 PHE A 320 TYR 0.029 0.001 TYR B 75 ARG 0.007 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 357) hydrogen bonds : angle 4.34308 ( 1062) SS BOND : bond 0.00144 ( 3) SS BOND : angle 1.17782 ( 6) covalent geometry : bond 0.00262 ( 7243) covalent geometry : angle 0.61156 ( 9793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9174 (tmm) cc_final: 0.8893 (tmm) REVERT: B 232 TRP cc_start: 0.8064 (m-10) cc_final: 0.7809 (m-10) REVERT: B 268 ASN cc_start: 0.8791 (t0) cc_final: 0.8527 (t0) REVERT: B 333 MET cc_start: 0.6875 (tpp) cc_final: 0.6491 (tmm) REVERT: C 79 MET cc_start: 0.8864 (mmp) cc_final: 0.8472 (mmm) REVERT: C 222 MET cc_start: 0.8625 (ppp) cc_final: 0.8326 (ppp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1646 time to fit residues: 24.6028 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.090492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064331 restraints weight = 27487.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066008 restraints weight = 16937.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067144 restraints weight = 12440.339| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7246 Z= 0.159 Angle : 0.629 7.952 9799 Z= 0.320 Chirality : 0.042 0.223 1064 Planarity : 0.005 0.099 1229 Dihedral : 4.571 19.506 928 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 850 helix: 1.57 (0.29), residues: 288 sheet: -0.22 (0.31), residues: 294 loop : -1.36 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 PHE 0.018 0.002 PHE C 234 TYR 0.021 0.001 TYR B 75 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 357) hydrogen bonds : angle 4.47749 ( 1062) SS BOND : bond 0.00218 ( 3) SS BOND : angle 1.40320 ( 6) covalent geometry : bond 0.00358 ( 7243) covalent geometry : angle 0.62841 ( 9793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9210 (tmm) cc_final: 0.8918 (tmm) REVERT: B 268 ASN cc_start: 0.8836 (t0) cc_final: 0.8634 (t0) REVERT: B 333 MET cc_start: 0.6898 (tpp) cc_final: 0.6516 (tmm) REVERT: C 79 MET cc_start: 0.8865 (mmp) cc_final: 0.8386 (mmm) REVERT: C 222 MET cc_start: 0.8603 (ppp) cc_final: 0.8295 (ppp) REVERT: C 321 LYS cc_start: 0.9700 (tptp) cc_final: 0.9487 (tptp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1606 time to fit residues: 22.9667 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.090924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065000 restraints weight = 27498.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066690 restraints weight = 16873.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067766 restraints weight = 12312.696| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7246 Z= 0.132 Angle : 0.625 8.677 9799 Z= 0.314 Chirality : 0.042 0.221 1064 Planarity : 0.005 0.097 1229 Dihedral : 4.581 23.140 928 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 850 helix: 1.59 (0.29), residues: 288 sheet: -0.19 (0.31), residues: 292 loop : -1.28 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 PHE 0.031 0.001 PHE A 316 TYR 0.019 0.001 TYR B 75 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 357) hydrogen bonds : angle 4.35966 ( 1062) SS BOND : bond 0.00130 ( 3) SS BOND : angle 1.27472 ( 6) covalent geometry : bond 0.00298 ( 7243) covalent geometry : angle 0.62437 ( 9793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.8900 (t0) cc_final: 0.8643 (t0) REVERT: B 333 MET cc_start: 0.6930 (tpp) cc_final: 0.6500 (tmm) REVERT: C 79 MET cc_start: 0.8863 (mmp) cc_final: 0.8383 (mmm) REVERT: C 222 MET cc_start: 0.8652 (ppp) cc_final: 0.8344 (ppp) REVERT: C 321 LYS cc_start: 0.9697 (tptp) cc_final: 0.9480 (tptp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1607 time to fit residues: 22.5817 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.090519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064168 restraints weight = 27122.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065813 restraints weight = 16707.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066934 restraints weight = 12311.390| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7246 Z= 0.141 Angle : 0.620 8.364 9799 Z= 0.314 Chirality : 0.042 0.217 1064 Planarity : 0.005 0.100 1229 Dihedral : 4.606 25.058 928 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.30), residues: 850 helix: 1.61 (0.29), residues: 288 sheet: -0.29 (0.30), residues: 301 loop : -1.31 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 232 HIS 0.010 0.001 HIS C 132 PHE 0.014 0.001 PHE C 234 TYR 0.016 0.001 TYR B 75 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 357) hydrogen bonds : angle 4.41853 ( 1062) SS BOND : bond 0.00148 ( 3) SS BOND : angle 1.30978 ( 6) covalent geometry : bond 0.00319 ( 7243) covalent geometry : angle 0.61957 ( 9793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.44 seconds wall clock time: 44 minutes 33.08 seconds (2673.08 seconds total)