Starting phenix.real_space_refine on Wed Mar 12 03:27:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/03_2025/8h8d_34543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/03_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_34543/03_2025/8h8d_34543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/03_2025/8h8d_34543.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/03_2025/8h8d_34543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/03_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-5624/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: 4.68, per 1000 atoms: 0.66 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: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 1.94 Time building geometry restraints manager: 1.73 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: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.250 Find NCS groups from input model: 0.310 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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 7243 Z= 0.288 Angle : 0.867 10.779 9793 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 *********************** 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 : 0.767 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: 0.1907 time to fit residues: 32.8795 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 : 0.760 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 ** 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 = 0.3717 r_free = 0.3717 target = 0.092169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065768 restraints weight = 26635.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067391 restraints weight = 16587.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068486 restraints weight = 12337.483| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7243 Z= 0.246 Angle : 0.655 8.185 9793 Z= 0.345 Chirality : 0.044 0.188 1064 Planarity : 0.005 0.059 1229 Dihedral : 4.861 20.224 928 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.30), residues: 850 helix: 1.30 (0.29), residues: 293 sheet: -0.43 (0.30), residues: 295 loop : -1.43 (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 0.023 0.002 PHE A 320 TYR 0.018 0.002 TYR B 158 ARG 0.027 0.001 ARG B 337 *********************** 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 138 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8733 (ptm) cc_final: 0.8477 (ppp) REVERT: B 158 TYR cc_start: 0.8075 (m-10) cc_final: 0.7822 (m-10) REVERT: B 333 MET cc_start: 0.6750 (tpp) cc_final: 0.6257 (tmm) REVERT: C 79 MET cc_start: 0.8802 (mmp) cc_final: 0.8510 (mmm) REVERT: C 112 TYR cc_start: 0.7223 (p90) cc_final: 0.6354 (p90) REVERT: C 169 HIS cc_start: 0.7779 (t-170) cc_final: 0.7576 (t-90) REVERT: C 233 LYS cc_start: 0.9025 (tptt) cc_final: 0.8763 (tptt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1793 time to fit residues: 33.9449 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 : 0.907 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** 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 = 0.3714 r_free = 0.3714 target = 0.092464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070189 restraints weight = 26764.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.070085 restraints weight = 18386.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070588 restraints weight = 16066.313| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7243 Z= 0.195 Angle : 0.614 7.352 9793 Z= 0.317 Chirality : 0.042 0.145 1064 Planarity : 0.004 0.075 1229 Dihedral : 4.760 20.746 928 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -0.28 (0.30), residues: 850 helix: 1.26 (0.29), residues: 291 sheet: -0.39 (0.30), residues: 297 loop : -1.48 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 232 HIS 0.004 0.001 HIS C 190 PHE 0.033 0.001 PHE C 325 TYR 0.018 0.001 TYR C 203 ARG 0.008 0.000 ARG C 177 *********************** 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 116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9125 (tmm) cc_final: 0.8875 (tmm) REVERT: B 222 MET cc_start: 0.7893 (tmm) cc_final: 0.7606 (tmm) REVERT: B 309 ILE cc_start: 0.9565 (tp) cc_final: 0.9342 (pt) REVERT: B 333 MET cc_start: 0.6915 (tpp) cc_final: 0.6358 (tmm) REVERT: C 79 MET cc_start: 0.8921 (mmp) cc_final: 0.8463 (mmm) REVERT: C 202 ASP cc_start: 0.7890 (t0) cc_final: 0.7667 (t0) REVERT: C 233 LYS cc_start: 0.8867 (tptt) cc_final: 0.8582 (tptt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1686 time to fit residues: 27.2939 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 : 0.837 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.092949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066924 restraints weight = 27001.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068528 restraints weight = 16799.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069667 restraints weight = 12471.467| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7243 Z= 0.166 Angle : 0.586 8.728 9793 Z= 0.300 Chirality : 0.042 0.157 1064 Planarity : 0.005 0.096 1229 Dihedral : 4.637 21.668 928 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 850 helix: 1.36 (0.29), residues: 290 sheet: -0.25 (0.30), residues: 296 loop : -1.44 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 232 HIS 0.002 0.001 HIS A 99 PHE 0.019 0.001 PHE C 325 TYR 0.015 0.001 TYR C 203 ARG 0.020 0.001 ARG B 181 *********************** 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 122 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.822 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: 0.9189 (tmm) cc_final: 0.8926 (tmm) REVERT: B 222 MET cc_start: 0.7936 (tmm) cc_final: 0.7655 (tmm) REVERT: B 309 ILE cc_start: 0.9525 (tp) cc_final: 0.9303 (pt) REVERT: B 333 MET cc_start: 0.6748 (tpp) cc_final: 0.6351 (tmm) REVERT: C 79 MET cc_start: 0.8838 (mmp) cc_final: 0.8422 (mmm) REVERT: C 202 ASP cc_start: 0.8150 (t0) cc_final: 0.7921 (t0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1607 time to fit residues: 27.5337 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 : 0.914 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.0060 chunk 57 optimal weight: 20.0000 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.092732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070104 restraints weight = 26607.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070253 restraints weight = 19418.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070621 restraints weight = 15236.859| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7243 Z= 0.170 Angle : 0.589 7.524 9793 Z= 0.301 Chirality : 0.042 0.155 1064 Planarity : 0.005 0.107 1229 Dihedral : 4.544 20.973 928 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.48 (0.29), residues: 288 sheet: -0.18 (0.31), residues: 296 loop : -1.36 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 232 HIS 0.012 0.001 HIS C 132 PHE 0.014 0.001 PHE A 320 TYR 0.016 0.001 TYR C 203 ARG 0.011 0.000 ARG B 181 *********************** 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 114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.899 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: 0.9170 (tmm) cc_final: 0.8905 (tmm) REVERT: B 222 MET cc_start: 0.7825 (tmm) cc_final: 0.7553 (tmm) REVERT: B 268 ASN cc_start: 0.8856 (t0) cc_final: 0.8592 (t0) REVERT: B 295 GLN cc_start: 0.8983 (mt0) cc_final: 0.8765 (tt0) REVERT: B 333 MET cc_start: 0.7111 (tpp) cc_final: 0.6661 (tmm) REVERT: C 79 MET cc_start: 0.8869 (mmp) cc_final: 0.8427 (mmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1518 time to fit residues: 24.6892 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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: 0.8980 chunk 80 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.091871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065594 restraints weight = 27072.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067246 restraints weight = 16898.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068298 restraints weight = 12496.403| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7243 Z= 0.189 Angle : 0.586 7.468 9793 Z= 0.301 Chirality : 0.041 0.150 1064 Planarity : 0.005 0.102 1229 Dihedral : 4.560 24.887 928 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 0.03 (0.30), residues: 850 helix: 1.56 (0.29), residues: 288 sheet: -0.14 (0.31), residues: 286 loop : -1.39 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 232 HIS 0.014 0.001 HIS C 132 PHE 0.022 0.001 PHE B 316 TYR 0.017 0.001 TYR C 203 ARG 0.010 0.000 ARG B 181 *********************** 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 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.768 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: 0.9131 (tmm) cc_final: 0.8852 (tmm) REVERT: A 316 PHE cc_start: 0.9273 (m-10) cc_final: 0.9061 (m-80) REVERT: B 295 GLN cc_start: 0.9061 (mt0) cc_final: 0.8726 (tt0) REVERT: B 333 MET cc_start: 0.6883 (tpp) cc_final: 0.6499 (tmm) REVERT: C 79 MET cc_start: 0.8826 (mmp) cc_final: 0.8380 (mmm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1516 time to fit residues: 24.8001 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 : 0.783 ------------------------------------------------------------------------------- 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: 0.7980 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064267 restraints weight = 26883.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065887 restraints weight = 16752.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066947 restraints weight = 12367.831| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7243 Z= 0.238 Angle : 0.619 9.126 9793 Z= 0.316 Chirality : 0.042 0.258 1064 Planarity : 0.005 0.126 1229 Dihedral : 4.744 25.960 928 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 1.52 (0.29), residues: 289 sheet: -0.24 (0.31), residues: 292 loop : -1.36 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 232 HIS 0.014 0.001 HIS C 132 PHE 0.018 0.001 PHE C 234 TYR 0.024 0.002 TYR B 158 ARG 0.011 0.001 ARG B 181 *********************** 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 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.9065 (tmm) cc_final: 0.8722 (tmm) REVERT: A 316 PHE cc_start: 0.9252 (m-10) cc_final: 0.9038 (m-80) REVERT: B 268 ASN cc_start: 0.8914 (t0) cc_final: 0.8621 (t0) REVERT: B 295 GLN cc_start: 0.9128 (mt0) cc_final: 0.8753 (mt0) REVERT: B 333 MET cc_start: 0.6961 (tpp) cc_final: 0.6555 (tmm) REVERT: C 79 MET cc_start: 0.8889 (mmp) cc_final: 0.8420 (mmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1409 time to fit residues: 21.6800 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 : 1.187 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.091237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065256 restraints weight = 26923.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066914 restraints weight = 16677.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.067953 restraints weight = 12246.765| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7243 Z= 0.171 Angle : 0.608 7.891 9793 Z= 0.306 Chirality : 0.043 0.227 1064 Planarity : 0.004 0.095 1229 Dihedral : 4.598 24.745 928 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.02 (0.30), residues: 850 helix: 1.56 (0.29), residues: 288 sheet: -0.19 (0.31), residues: 293 loop : -1.46 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 232 HIS 0.012 0.001 HIS C 132 PHE 0.020 0.001 PHE B 316 TYR 0.018 0.001 TYR C 203 ARG 0.009 0.000 ARG B 181 *********************** 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 112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.9256 (m-10) cc_final: 0.9039 (m-80) REVERT: B 222 MET cc_start: 0.7912 (tmm) cc_final: 0.7653 (tmm) REVERT: B 268 ASN cc_start: 0.8942 (t0) cc_final: 0.8591 (t0) REVERT: B 295 GLN cc_start: 0.9114 (mt0) cc_final: 0.8802 (mt0) REVERT: B 333 MET cc_start: 0.6867 (tpp) cc_final: 0.6492 (tmm) REVERT: C 79 MET cc_start: 0.8869 (mmp) cc_final: 0.8415 (mmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1467 time to fit residues: 23.5747 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.089939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066312 restraints weight = 27695.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066917 restraints weight = 20224.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067239 restraints weight = 14559.157| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7243 Z= 0.235 Angle : 0.646 8.040 9793 Z= 0.326 Chirality : 0.042 0.224 1064 Planarity : 0.005 0.109 1229 Dihedral : 4.744 25.602 928 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.11 (0.30), residues: 850 helix: 1.52 (0.29), residues: 288 sheet: -0.35 (0.31), residues: 294 loop : -1.43 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 232 HIS 0.012 0.001 HIS C 132 PHE 0.011 0.002 PHE B 198 TYR 0.030 0.002 TYR B 75 ARG 0.010 0.000 ARG B 181 *********************** 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 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.9158 (m-10) cc_final: 0.8957 (m-80) REVERT: B 222 MET cc_start: 0.7953 (tmm) cc_final: 0.7728 (tmm) REVERT: B 268 ASN cc_start: 0.8922 (t0) cc_final: 0.8580 (t0) REVERT: B 295 GLN cc_start: 0.9125 (mt0) cc_final: 0.8795 (mt0) REVERT: B 333 MET cc_start: 0.7074 (tpp) cc_final: 0.6635 (tmm) REVERT: C 79 MET cc_start: 0.8888 (mmp) cc_final: 0.8391 (mmm) REVERT: C 321 LYS cc_start: 0.9635 (tptp) cc_final: 0.9421 (tptp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1508 time to fit residues: 22.5584 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065297 restraints weight = 27719.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066977 restraints weight = 17105.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068117 restraints weight = 12580.689| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7243 Z= 0.171 Angle : 0.637 8.522 9793 Z= 0.317 Chirality : 0.043 0.218 1064 Planarity : 0.004 0.092 1229 Dihedral : 4.623 24.749 928 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.30), residues: 850 helix: 1.51 (0.29), residues: 288 sheet: -0.26 (0.31), residues: 291 loop : -1.37 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 232 HIS 0.011 0.001 HIS C 132 PHE 0.021 0.001 PHE B 316 TYR 0.025 0.001 TYR B 75 ARG 0.009 0.000 ARG B 181 ********************** 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 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.9243 (m-10) cc_final: 0.9007 (m-80) REVERT: B 295 GLN cc_start: 0.9155 (mt0) cc_final: 0.8813 (mt0) REVERT: B 333 MET cc_start: 0.6921 (tpp) cc_final: 0.6496 (tmm) REVERT: C 79 MET cc_start: 0.8868 (mmp) cc_final: 0.8387 (mmm) REVERT: C 321 LYS cc_start: 0.9669 (tptp) cc_final: 0.9442 (tptp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1429 time to fit residues: 22.2524 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 : 0.838 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.090322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066522 restraints weight = 27071.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067226 restraints weight = 18963.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067519 restraints weight = 13983.829| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7243 Z= 0.212 Angle : 0.640 8.477 9793 Z= 0.320 Chirality : 0.042 0.216 1064 Planarity : 0.005 0.104 1229 Dihedral : 4.624 25.675 928 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.30), residues: 850 helix: 1.48 (0.29), residues: 288 sheet: -0.29 (0.31), residues: 293 loop : -1.35 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 232 HIS 0.011 0.001 HIS C 132 PHE 0.015 0.001 PHE C 234 TYR 0.023 0.002 TYR B 75 ARG 0.010 0.000 ARG B 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.15 seconds wall clock time: 43 minutes 12.89 seconds (2592.89 seconds total)