Starting phenix.real_space_refine on Tue Feb 11 15:01:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtu_24689/02_2025/7rtu_24689.cif" } resolution = 3.89 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= 0.000 sd= 1.000 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 48 5.16 5 C 3829 2.51 5 N 959 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3053 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain breaks: 1 Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2755 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 6, 'TRANS': 352} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.80, per 1000 atoms: 0.81 Number of scatterers: 5962 At special positions: 0 Unit cell: (74.705, 60.21, 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 48 16.00 O 1126 8.00 N 959 7.00 C 3829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.02 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 129 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 129 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 894.2 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 38 through 73 removed outlier: 3.727A pdb=" N LEU A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 162 removed outlier: 4.419A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 removed outlier: 4.423A pdb=" N THR A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 245 through 276 removed outlier: 3.766A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.553A pdb=" N THR A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 365 removed outlier: 4.179A pdb=" N GLY A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.486A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 Proline residue: A 411 - end of helix removed outlier: 3.860A pdb=" N TRP A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 71 removed outlier: 4.519A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 45 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 162 removed outlier: 3.556A pdb=" N ILE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.711A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 236 removed outlier: 3.658A pdb=" N THR B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 245 through 276 removed outlier: 4.081A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.718A pdb=" N THR B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 333 Processing helix chain 'B' and resid 338 through 365 removed outlier: 3.849A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 414 removed outlier: 4.394A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Proline residue: B 411 - end of helix 547 hydrogen bonds defined for protein. 1641 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: 1.76 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1866 1.34 - 1.46: 1093 1.46 - 1.58: 3048 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6073 Sorted by residual: bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.546 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 6068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8084 1.69 - 3.37: 133 3.37 - 5.06: 38 5.06 - 6.75: 12 6.75 - 8.44: 2 Bond angle restraints: 8269 Sorted by residual: angle pdb=" N VAL B 194 " pdb=" CA VAL B 194 " pdb=" C VAL B 194 " ideal model delta sigma weight residual 112.96 109.08 3.88 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 104.26 8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" C LYS B 147 " pdb=" N VAL B 148 " pdb=" CA VAL B 148 " ideal model delta sigma weight residual 122.97 120.53 2.44 9.80e-01 1.04e+00 6.20e+00 angle pdb=" C MET A 174 " pdb=" CA MET A 174 " pdb=" CB MET A 174 " ideal model delta sigma weight residual 109.99 114.49 -4.50 2.09e+00 2.29e-01 4.64e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.56 6.39 3.00e+00 1.11e-01 4.53e+00 ... (remaining 8264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 3342 22.27 - 44.54: 280 44.54 - 66.82: 36 66.82 - 89.09: 37 89.09 - 111.36: 25 Dihedral angle restraints: 3720 sinusoidal: 1537 harmonic: 2183 Sorted by residual: dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual 93.00 46.08 46.92 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual -175.09 -63.73 -111.36 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 NAG F 2 " pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" O3 NAG F 2 " ideal model delta sinusoidal sigma weight residual -175.09 -64.78 -110.31 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 3717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 913 0.056 - 0.112: 108 0.112 - 0.168: 9 0.168 - 0.224: 0 0.224 - 0.280: 7 Chirality restraints: 1037 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1034 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 381 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C ILE B 381 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE B 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS B 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 337 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 338 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 379 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR A 379 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 379 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 380 " -0.008 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 179 2.72 - 3.26: 6387 3.26 - 3.81: 10502 3.81 - 4.35: 10390 4.35 - 4.90: 18898 Nonbonded interactions: 46356 Sorted by model distance: nonbonded pdb=" O TYR A 280 " pdb=" ND2 ASN A 284 " model vdw 2.175 3.120 nonbonded pdb=" O ILE A 9 " pdb=" OH TYR A 383 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 212 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASN B 111 " pdb=" NH1 ARG B 212 " model vdw 2.257 3.120 nonbonded pdb=" OD1 ASP A 223 " pdb=" OG1 THR A 252 " model vdw 2.293 3.040 ... (remaining 46351 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 39 through 71 or resid 89 through 414)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'D' selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'F' } 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: 6.290 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 18.470 Find NCS groups from input model: 0.230 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 0.003 0.033 6073 Z= 0.221 Angle : 0.609 8.436 8269 Z= 0.281 Chirality : 0.042 0.280 1037 Planarity : 0.003 0.035 1005 Dihedral : 20.840 111.361 2304 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.37 % 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: 4.32 (0.31), residues: 746 helix: 3.15 (0.20), residues: 662 sheet: None (None), residues: 0 loop : 0.02 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 12 HIS 0.004 0.001 HIS A 18 PHE 0.013 0.001 PHE A 395 TYR 0.010 0.001 TYR B 216 ARG 0.004 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.595 Fit side-chains REVERT: B 135 MET cc_start: 0.7798 (ttm) cc_final: 0.7239 (ttm) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1828 time to fit residues: 20.0666 Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.210608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.199328 restraints weight = 6604.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186846 restraints weight = 11502.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186738 restraints weight = 11009.485| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6073 Z= 0.278 Angle : 0.638 6.672 8269 Z= 0.308 Chirality : 0.045 0.321 1037 Planarity : 0.004 0.040 1005 Dihedral : 15.305 88.210 1044 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.10 % Allowed : 11.77 % Favored : 87.13 % 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: 3.89 (0.30), residues: 746 helix: 2.86 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.21 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.006 0.001 HIS A 22 PHE 0.011 0.001 PHE A 403 TYR 0.014 0.002 TYR B 216 ARG 0.007 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.657 Fit side-chains REVERT: B 147 LYS cc_start: 0.7492 (ttmm) cc_final: 0.6999 (ttmt) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1790 time to fit residues: 18.2608 Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.214531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.200694 restraints weight = 6552.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.198853 restraints weight = 10711.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.198218 restraints weight = 9717.777| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6073 Z= 0.172 Angle : 0.526 6.898 8269 Z= 0.252 Chirality : 0.039 0.274 1037 Planarity : 0.003 0.036 1005 Dihedral : 12.638 78.238 1044 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.78 % Allowed : 17.11 % Favored : 82.10 % 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: 4.17 (0.30), residues: 746 helix: 3.07 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.42 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 PHE 0.008 0.001 PHE A 395 TYR 0.008 0.001 TYR A 216 ARG 0.005 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.623 Fit side-chains REVERT: A 147 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7737 (ttmm) REVERT: B 147 LYS cc_start: 0.7336 (ttmm) cc_final: 0.6830 (ttmt) REVERT: B 298 LEU cc_start: 0.8084 (mm) cc_final: 0.7748 (mm) outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1715 time to fit residues: 17.0912 Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.210621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.196778 restraints weight = 6784.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.190978 restraints weight = 11252.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.187009 restraints weight = 7785.491| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6073 Z= 0.240 Angle : 0.568 7.581 8269 Z= 0.275 Chirality : 0.041 0.309 1037 Planarity : 0.003 0.037 1005 Dihedral : 11.216 70.179 1044 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.83 % Allowed : 17.43 % Favored : 79.75 % 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: 3.99 (0.30), residues: 746 helix: 2.95 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.45 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.004 0.001 HIS A 22 PHE 0.008 0.001 PHE A 395 TYR 0.012 0.001 TYR B 216 ARG 0.003 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.585 Fit side-chains REVERT: A 324 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 138 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 298 LEU cc_start: 0.8273 (mm) cc_final: 0.7891 (mm) REVERT: B 324 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7205 (tt) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 0.1757 time to fit residues: 20.5683 Evaluate side-chains 81 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 324 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.211688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.201063 restraints weight = 6594.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.189367 restraints weight = 9783.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186884 restraints weight = 7584.158| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6073 Z= 0.201 Angle : 0.558 8.160 8269 Z= 0.266 Chirality : 0.040 0.293 1037 Planarity : 0.003 0.037 1005 Dihedral : 9.975 60.406 1044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.83 % Allowed : 19.62 % Favored : 77.55 % 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: 4.09 (0.30), residues: 746 helix: 3.02 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.48 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.003 0.001 HIS A 299 PHE 0.008 0.001 PHE A 395 TYR 0.009 0.001 TYR B 216 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.620 Fit side-chains REVERT: A 322 MET cc_start: 0.7911 (tpp) cc_final: 0.7280 (mtt) REVERT: A 324 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7840 (tt) REVERT: B 138 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 147 LYS cc_start: 0.7291 (ttmm) cc_final: 0.6919 (ttmt) REVERT: B 298 LEU cc_start: 0.8245 (mm) cc_final: 0.7856 (mm) REVERT: B 351 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8498 (mm) outliers start: 18 outliers final: 8 residues processed: 84 average time/residue: 0.1635 time to fit residues: 18.6786 Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.211191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.197363 restraints weight = 6561.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194818 restraints weight = 11488.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.193546 restraints weight = 11005.493| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6073 Z= 0.209 Angle : 0.566 8.308 8269 Z= 0.269 Chirality : 0.040 0.300 1037 Planarity : 0.003 0.037 1005 Dihedral : 8.967 56.639 1044 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.51 % Allowed : 20.25 % Favored : 77.24 % 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: 4.08 (0.30), residues: 746 helix: 3.01 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.44 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 PHE 0.008 0.001 PHE A 395 TYR 0.010 0.001 TYR B 216 ARG 0.003 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.621 Fit side-chains REVERT: A 322 MET cc_start: 0.7934 (tpp) cc_final: 0.7381 (mtt) REVERT: A 324 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7798 (tt) REVERT: B 138 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (mp) REVERT: B 219 LEU cc_start: 0.7071 (tt) cc_final: 0.6639 (tp) REVERT: B 298 LEU cc_start: 0.8140 (mm) cc_final: 0.7801 (mm) REVERT: B 324 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7235 (tt) REVERT: B 351 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8513 (mm) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.1725 time to fit residues: 19.1583 Evaluate side-chains 80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 63 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.0170 chunk 34 optimal weight: 0.0980 overall best weight: 0.1818 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.216970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.205036 restraints weight = 6551.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.194336 restraints weight = 12085.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.193708 restraints weight = 10956.590| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6073 Z= 0.135 Angle : 0.519 7.633 8269 Z= 0.246 Chirality : 0.036 0.266 1037 Planarity : 0.003 0.036 1005 Dihedral : 8.014 59.547 1044 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 20.57 % Favored : 77.55 % 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: 4.44 (0.30), residues: 746 helix: 3.26 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.49 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.005 0.001 HIS A 299 PHE 0.007 0.001 PHE A 34 TYR 0.006 0.001 TYR A 8 ARG 0.002 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.665 Fit side-chains REVERT: A 322 MET cc_start: 0.7845 (tpp) cc_final: 0.7351 (mtt) REVERT: B 147 LYS cc_start: 0.7257 (ttmm) cc_final: 0.6862 (ttmt) REVERT: B 298 LEU cc_start: 0.8174 (mm) cc_final: 0.7830 (mm) REVERT: B 324 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7126 (tt) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.1789 time to fit residues: 20.5290 Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.213676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.202029 restraints weight = 6547.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.192631 restraints weight = 11288.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.188978 restraints weight = 8180.655| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6073 Z= 0.188 Angle : 0.567 8.041 8269 Z= 0.265 Chirality : 0.039 0.296 1037 Planarity : 0.003 0.036 1005 Dihedral : 7.661 59.383 1044 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.67 % Allowed : 20.25 % Favored : 77.08 % 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: 4.31 (0.30), residues: 746 helix: 3.18 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.47 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 PHE 0.007 0.001 PHE A 395 TYR 0.008 0.001 TYR B 216 ARG 0.002 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.540 Fit side-chains REVERT: A 322 MET cc_start: 0.7941 (tpp) cc_final: 0.7435 (mtt) REVERT: A 324 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7834 (tt) REVERT: B 298 LEU cc_start: 0.8208 (mm) cc_final: 0.7838 (mm) REVERT: B 324 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7193 (tt) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.1666 time to fit residues: 18.6279 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.0010 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.214642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.203671 restraints weight = 6553.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193210 restraints weight = 11180.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.191455 restraints weight = 8177.024| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6073 Z= 0.167 Angle : 0.564 8.932 8269 Z= 0.263 Chirality : 0.038 0.290 1037 Planarity : 0.003 0.036 1005 Dihedral : 7.409 59.881 1044 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.20 % Allowed : 20.88 % Favored : 76.92 % 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: 4.32 (0.30), residues: 746 helix: 3.18 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.53 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 PHE 0.007 0.001 PHE A 395 TYR 0.008 0.001 TYR B 216 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.616 Fit side-chains REVERT: A 322 MET cc_start: 0.7888 (tpp) cc_final: 0.7399 (mtt) REVERT: A 324 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 147 LYS cc_start: 0.7676 (tppt) cc_final: 0.7141 (ttmt) REVERT: B 298 LEU cc_start: 0.8245 (mm) cc_final: 0.7844 (mm) REVERT: B 324 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7152 (tt) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.1694 time to fit residues: 17.9258 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.212948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.204566 restraints weight = 6549.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.190067 restraints weight = 11021.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.189258 restraints weight = 8768.158| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6073 Z= 0.276 Angle : 0.631 7.875 8269 Z= 0.302 Chirality : 0.042 0.331 1037 Planarity : 0.003 0.035 1005 Dihedral : 7.354 58.816 1044 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 20.72 % Favored : 77.08 % 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: 3.95 (0.30), residues: 746 helix: 2.94 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.55 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 22 PHE 0.012 0.001 PHE A 315 TYR 0.013 0.001 TYR A 216 ARG 0.003 0.000 ARG B 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.7936 (tpp) cc_final: 0.7568 (mtt) REVERT: A 324 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 298 LEU cc_start: 0.8253 (mm) cc_final: 0.7820 (mm) REVERT: B 324 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7368 (tt) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1732 time to fit residues: 17.3931 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.217738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.209111 restraints weight = 6576.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.195752 restraints weight = 10851.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193007 restraints weight = 9975.148| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6073 Z= 0.161 Angle : 0.566 8.871 8269 Z= 0.266 Chirality : 0.038 0.291 1037 Planarity : 0.003 0.036 1005 Dihedral : 7.016 55.184 1044 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.88 % Allowed : 21.35 % Favored : 76.77 % 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: 4.23 (0.30), residues: 746 helix: 3.13 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.58 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 PHE 0.007 0.001 PHE A 395 TYR 0.009 0.001 TYR B 216 ARG 0.006 0.000 ARG B 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.18 seconds wall clock time: 34 minutes 30.97 seconds (2070.97 seconds total)