Starting phenix.real_space_refine on Thu Jul 2 02:48:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtu_24689/07_2026/7rtu_24689.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 chiralities: 3 Time building chain proxies: 1.51, per 1000 atoms: 0.25 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: 0.64 Conformation dependent library (CDL) restraints added in 366.1 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: 0.14 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: 1.11 Time building geometry restraints manager: 0.83 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 - 15.08: 3012 15.08 - 30.15: 332 30.15 - 45.23: 113 45.23 - 60.31: 20 60.31 - 75.38: 3 Dihedral angle restraints: 3480 sinusoidal: 1297 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=" CA MET B 118 " pdb=" C MET B 118 " pdb=" N HIS B 119 " pdb=" CA HIS B 119 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB MET B 275 " pdb=" CG MET B 275 " pdb=" SD MET B 275 " pdb=" CE MET B 275 " ideal model delta sinusoidal sigma weight residual -180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3477 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 6089 Z= 0.165 Angle : 0.621 8.436 8313 Z= 0.284 Chirality : 0.042 0.280 1037 Planarity : 0.003 0.035 1005 Dihedral : 14.311 75.382 2064 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG B 295 TYR 0.010 0.001 TYR B 216 PHE 0.013 0.001 PHE A 395 TRP 0.013 0.001 TRP A 12 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6073) covalent geometry : angle 0.60857 / 0.28 ( 8269) SS BOND : bond 0.00424 / 0.22 ( 4) SS BOND : angle 0.64752 / 0.39 ( 8) hydrogen bonds : bond 0.07108 / 5.02 ( 547) hydrogen bonds : angle 3.84594 / 2.90 ( 1641) link_BETA1-4 : bond 0.00400 / 0.19 ( 8) link_BETA1-4 : angle 1.62394 / 1.18 ( 24) link_NAG-ASN : bond 0.00341 / 0.17 ( 4) link_NAG-ASN : angle 2.58007 / 1.59 ( 12) *********************** 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 : 0.140 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: 0.0648 time to fit residues: 7.2853 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN ** B 325 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 = 0.4496 r_free = 0.4496 target = 0.213505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.4267 r_free = 0.4267 target = 0.190240 restraints weight = 6634.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190316 restraints weight = 7180.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190335 restraints weight = 6436.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190335 restraints weight = 6332.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190337 restraints weight = 6332.652| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6089 Z= 0.155 Angle : 0.555 6.874 8313 Z= 0.273 Chirality : 0.039 0.308 1037 Planarity : 0.003 0.038 1005 Dihedral : 3.682 14.845 804 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.26 % Allowed : 10.36 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.30), residues: 746 helix: 3.01 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.12 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.010 0.001 TYR A 207 PHE 0.012 0.001 PHE A 403 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6073) covalent geometry : angle 0.53703 / 0.27 ( 8269) SS BOND : bond 0.00492 / 0.26 ( 4) SS BOND : angle 0.47207 / 0.26 ( 8) hydrogen bonds : bond 0.03450 / 2.34 ( 547) hydrogen bonds : angle 3.52112 / 2.63 ( 1641) link_BETA1-4 : bond 0.00528 / 0.23 ( 8) link_BETA1-4 : angle 1.91577 / 1.38 ( 24) link_NAG-ASN : bond 0.00151 / 0.08 ( 4) link_NAG-ASN : angle 2.66795 / 1.67 ( 12) *********************** 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 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.208 Fit side-chains REVERT: B 147 LYS cc_start: 0.7452 (ttmm) cc_final: 0.6952 (ttmt) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.0729 time to fit residues: 7.3198 Evaluate side-chains 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 199 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 2 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.210458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.196768 restraints weight = 6653.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.188406 restraints weight = 11126.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184827 restraints weight = 7905.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.184619 restraints weight = 9275.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.184707 restraints weight = 7190.257| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6089 Z= 0.171 Angle : 0.563 6.841 8313 Z= 0.278 Chirality : 0.039 0.305 1037 Planarity : 0.003 0.040 1005 Dihedral : 3.757 14.858 804 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.41 % Allowed : 16.01 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.30), residues: 746 helix: 2.91 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.43 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.015 0.001 TYR B 216 PHE 0.009 0.001 PHE A 395 TRP 0.010 0.001 TRP B 213 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6073) covalent geometry : angle 0.54476 / 0.27 ( 8269) SS BOND : bond 0.00588 / 0.30 ( 4) SS BOND : angle 0.56347 / 0.33 ( 8) hydrogen bonds : bond 0.03475 / 2.37 ( 547) hydrogen bonds : angle 3.55295 / 2.66 ( 1641) link_BETA1-4 : bond 0.00475 / 0.21 ( 8) link_BETA1-4 : angle 1.90833 / 1.37 ( 24) link_NAG-ASN : bond 0.00122 / 0.06 ( 4) link_NAG-ASN : angle 2.79745 / 1.78 ( 12) *********************** 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 82 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: B 147 LYS cc_start: 0.7452 (ttmm) cc_final: 0.6945 (ttmt) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.0672 time to fit residues: 7.2389 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 : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 229 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.205587 restraints weight = 6528.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188940 restraints weight = 11364.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.190341 restraints weight = 8475.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.191600 restraints weight = 6737.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191679 restraints weight = 6340.496| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6089 Z= 0.150 Angle : 0.527 6.855 8313 Z= 0.260 Chirality : 0.038 0.295 1037 Planarity : 0.003 0.040 1005 Dihedral : 3.706 14.592 804 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.83 % Allowed : 16.64 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.98 (0.30), residues: 746 helix: 2.93 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.41 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 212 TYR 0.012 0.001 TYR B 216 PHE 0.008 0.001 PHE A 395 TRP 0.009 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6073) covalent geometry : angle 0.50715 / 0.26 ( 8269) SS BOND : bond 0.00519 / 0.27 ( 4) SS BOND : angle 0.46071 / 0.26 ( 8) hydrogen bonds : bond 0.03332 / 2.28 ( 547) hydrogen bonds : angle 3.49405 / 2.61 ( 1641) link_BETA1-4 : bond 0.00474 / 0.21 ( 8) link_BETA1-4 : angle 1.87070 / 1.34 ( 24) link_NAG-ASN : bond 0.00158 / 0.08 ( 4) link_NAG-ASN : angle 2.77586 / 1.77 ( 12) *********************** 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 89 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.317 Fit side-chains REVERT: A 324 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 138 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 298 LEU cc_start: 0.8256 (mm) cc_final: 0.7880 (mm) REVERT: B 324 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7269 (tt) outliers start: 18 outliers final: 6 residues processed: 83 average time/residue: 0.0696 time to fit residues: 8.0176 Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 53 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.215596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.203686 restraints weight = 6617.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.202283 restraints weight = 11307.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.200797 restraints weight = 10292.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.198201 restraints weight = 11485.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.198129 restraints weight = 10576.064| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6089 Z= 0.128 Angle : 0.516 6.881 8313 Z= 0.251 Chirality : 0.037 0.285 1037 Planarity : 0.003 0.038 1005 Dihedral : 3.629 14.300 804 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.51 % Allowed : 18.37 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.30), residues: 746 helix: 3.05 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.45 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.008 0.001 TYR B 216 PHE 0.008 0.001 PHE A 395 TRP 0.009 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6073) covalent geometry : angle 0.49654 / 0.25 ( 8269) SS BOND : bond 0.00373 / 0.19 ( 4) SS BOND : angle 0.41702 / 0.24 ( 8) hydrogen bonds : bond 0.03201 / 2.19 ( 547) hydrogen bonds : angle 3.43039 / 2.57 ( 1641) link_BETA1-4 : bond 0.00490 / 0.22 ( 8) link_BETA1-4 : angle 1.82512 / 1.31 ( 24) link_NAG-ASN : bond 0.00229 / 0.11 ( 4) link_NAG-ASN : angle 2.73976 / 1.76 ( 12) *********************** 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 87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.161 Fit side-chains REVERT: A 322 MET cc_start: 0.7806 (tpp) cc_final: 0.7253 (mtt) REVERT: B 138 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 147 LYS cc_start: 0.7332 (ttmm) cc_final: 0.6953 (ttmt) REVERT: B 298 LEU cc_start: 0.8083 (mm) cc_final: 0.7703 (mm) REVERT: B 351 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (mm) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.0556 time to fit residues: 6.2610 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.212897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192269 restraints weight = 6564.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191980 restraints weight = 7643.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192293 restraints weight = 6176.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192314 restraints weight = 5790.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192313 restraints weight = 5602.021| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6089 Z= 0.170 Angle : 0.573 6.817 8313 Z= 0.279 Chirality : 0.040 0.306 1037 Planarity : 0.003 0.040 1005 Dihedral : 3.739 14.707 804 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.98 % Allowed : 19.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.92 (0.30), residues: 746 helix: 2.90 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.47 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.011 0.001 TYR B 216 PHE 0.008 0.001 PHE A 395 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6073) covalent geometry : angle 0.55569 / 0.28 ( 8269) SS BOND : bond 0.00546 / 0.28 ( 4) SS BOND : angle 0.52256 / 0.29 ( 8) hydrogen bonds : bond 0.03397 / 2.32 ( 547) hydrogen bonds : angle 3.51438 / 2.63 ( 1641) link_BETA1-4 : bond 0.00441 / 0.20 ( 8) link_BETA1-4 : angle 1.82885 / 1.30 ( 24) link_NAG-ASN : bond 0.00129 / 0.07 ( 4) link_NAG-ASN : angle 2.85429 / 1.86 ( 12) *********************** 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 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.124 Fit side-chains REVERT: A 322 MET cc_start: 0.7965 (tpp) cc_final: 0.7481 (mtt) REVERT: A 324 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 138 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 298 LEU cc_start: 0.8227 (mm) cc_final: 0.7851 (mm) REVERT: B 324 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7329 (tt) REVERT: B 351 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8491 (mm) outliers start: 19 outliers final: 11 residues processed: 85 average time/residue: 0.0618 time to fit residues: 7.0436 Evaluate side-chains 83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 229 VAL 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 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 66 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.213428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201068 restraints weight = 6539.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.198915 restraints weight = 12492.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.197190 restraints weight = 13033.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.189980 restraints weight = 12480.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.187526 restraints weight = 8839.322| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6089 Z= 0.150 Angle : 0.557 6.812 8313 Z= 0.272 Chirality : 0.039 0.296 1037 Planarity : 0.003 0.040 1005 Dihedral : 3.735 14.554 804 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.14 % Allowed : 19.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.30), residues: 746 helix: 2.97 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.50 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.010 0.001 TYR B 216 PHE 0.010 0.001 PHE A 315 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6073) covalent geometry : angle 0.53855 / 0.27 ( 8269) SS BOND : bond 0.00473 / 0.25 ( 4) SS BOND : angle 0.46611 / 0.27 ( 8) hydrogen bonds : bond 0.03331 / 2.28 ( 547) hydrogen bonds : angle 3.49302 / 2.61 ( 1641) link_BETA1-4 : bond 0.00475 / 0.22 ( 8) link_BETA1-4 : angle 1.80486 / 1.28 ( 24) link_NAG-ASN : bond 0.00167 / 0.08 ( 4) link_NAG-ASN : angle 2.86167 / 1.86 ( 12) *********************** 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 88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.213 Fit side-chains REVERT: A 322 MET cc_start: 0.7940 (tpp) cc_final: 0.7569 (mtt) REVERT: A 324 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 138 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 147 LYS cc_start: 0.7303 (ttmm) cc_final: 0.6896 (ttmt) REVERT: B 298 LEU cc_start: 0.8289 (mm) cc_final: 0.7902 (mm) REVERT: B 324 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7202 (tt) REVERT: B 351 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8461 (mm) outliers start: 20 outliers final: 13 residues processed: 83 average time/residue: 0.0588 time to fit residues: 6.8191 Evaluate side-chains 83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU 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 229 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.0770 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.216608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.205820 restraints weight = 6475.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.195288 restraints weight = 10513.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192491 restraints weight = 8368.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.193043 restraints weight = 8660.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.193471 restraints weight = 6654.860| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6089 Z= 0.117 Angle : 0.521 6.894 8313 Z= 0.252 Chirality : 0.037 0.280 1037 Planarity : 0.003 0.039 1005 Dihedral : 3.623 14.896 804 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.98 % Allowed : 20.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.25 (0.30), residues: 746 helix: 3.13 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.46 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.008 0.001 TYR B 216 PHE 0.007 0.001 PHE A 308 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6073) covalent geometry : angle 0.50303 / 0.25 ( 8269) SS BOND : bond 0.00306 / 0.16 ( 4) SS BOND : angle 0.42713 / 0.24 ( 8) hydrogen bonds : bond 0.03120 / 2.13 ( 547) hydrogen bonds : angle 3.40575 / 2.55 ( 1641) link_BETA1-4 : bond 0.00512 / 0.23 ( 8) link_BETA1-4 : angle 1.76576 / 1.26 ( 24) link_NAG-ASN : bond 0.00309 / 0.15 ( 4) link_NAG-ASN : angle 2.73820 / 1.77 ( 12) *********************** 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: 19 poor density : 66 time to evaluate : 0.206 Fit side-chains REVERT: A 322 MET cc_start: 0.7902 (tpp) cc_final: 0.7506 (mtt) REVERT: A 324 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7826 (tt) REVERT: B 147 LYS cc_start: 0.7256 (ttmm) cc_final: 0.6857 (ttmt) REVERT: B 298 LEU cc_start: 0.8182 (mm) cc_final: 0.7850 (mm) REVERT: B 324 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7158 (tt) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 0.0652 time to fit residues: 7.3123 Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 229 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.214317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.203183 restraints weight = 6576.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.201021 restraints weight = 10747.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.199944 restraints weight = 11175.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.197869 restraints weight = 11191.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.190614 restraints weight = 9918.560| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6089 Z= 0.142 Angle : 0.556 6.841 8313 Z= 0.268 Chirality : 0.038 0.294 1037 Planarity : 0.003 0.038 1005 Dihedral : 3.662 15.410 804 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 19.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.30), residues: 746 helix: 3.07 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.54 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.009 0.001 TYR B 216 PHE 0.008 0.001 PHE A 395 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6073) covalent geometry : angle 0.53806 / 0.26 ( 8269) SS BOND : bond 0.00418 / 0.22 ( 4) SS BOND : angle 0.43775 / 0.26 ( 8) hydrogen bonds : bond 0.03245 / 2.22 ( 547) hydrogen bonds : angle 3.46091 / 2.59 ( 1641) link_BETA1-4 : bond 0.00471 / 0.21 ( 8) link_BETA1-4 : angle 1.77727 / 1.26 ( 24) link_NAG-ASN : bond 0.00196 / 0.10 ( 4) link_NAG-ASN : angle 2.80408 / 1.85 ( 12) *********************** 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 86 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.227 Fit side-chains REVERT: A 322 MET cc_start: 0.7921 (tpp) cc_final: 0.7484 (mtt) REVERT: A 324 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7871 (tt) REVERT: B 138 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 147 LYS cc_start: 0.7244 (ttmm) cc_final: 0.6856 (ttmt) REVERT: B 298 LEU cc_start: 0.8257 (mm) cc_final: 0.7915 (mm) REVERT: B 324 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7238 (tt) outliers start: 21 outliers final: 12 residues processed: 82 average time/residue: 0.0662 time to fit residues: 7.4695 Evaluate side-chains 81 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 229 VAL 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 138 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 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 42 optimal weight: 0.0470 chunk 54 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.216520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.207491 restraints weight = 6595.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191107 restraints weight = 10362.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.191824 restraints weight = 8967.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.192675 restraints weight = 7268.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.192910 restraints weight = 6493.526| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6089 Z= 0.124 Angle : 0.537 6.869 8313 Z= 0.259 Chirality : 0.037 0.285 1037 Planarity : 0.003 0.039 1005 Dihedral : 3.627 15.842 804 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.51 % Allowed : 20.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.30), residues: 746 helix: 3.13 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.55 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.008 0.001 TYR B 216 PHE 0.007 0.001 PHE A 395 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6073) covalent geometry : angle 0.51940 / 0.25 ( 8269) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 0.38021 / 0.22 ( 8) hydrogen bonds : bond 0.03172 / 2.17 ( 547) hydrogen bonds : angle 3.43303 / 2.57 ( 1641) link_BETA1-4 : bond 0.00489 / 0.22 ( 8) link_BETA1-4 : angle 1.75509 / 1.25 ( 24) link_NAG-ASN : bond 0.00296 / 0.15 ( 4) link_NAG-ASN : angle 2.75047 / 1.78 ( 12) ********************** 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 82 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.216 Fit side-chains REVERT: A 322 MET cc_start: 0.7863 (tpp) cc_final: 0.7474 (mtt) REVERT: A 324 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 138 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 147 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6776 (ttmt) REVERT: B 177 MET cc_start: 0.7564 (mmm) cc_final: 0.7364 (tpt) REVERT: B 298 LEU cc_start: 0.8202 (mm) cc_final: 0.7848 (mm) REVERT: B 324 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7219 (tt) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.0702 time to fit residues: 7.5222 Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 229 VAL 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 138 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 65 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.215603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.206430 restraints weight = 6549.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.188981 restraints weight = 10539.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.191511 restraints weight = 8613.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.191162 restraints weight = 7085.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.193062 restraints weight = 6518.930| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6089 Z= 0.136 Angle : 0.563 8.151 8313 Z= 0.268 Chirality : 0.039 0.294 1037 Planarity : 0.003 0.038 1005 Dihedral : 3.669 17.675 804 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.20 % Allowed : 21.19 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.18 (0.30), residues: 746 helix: 3.10 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.60 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.009 0.001 TYR B 216 PHE 0.007 0.001 PHE A 395 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6073) covalent geometry : angle 0.54666 / 0.26 ( 8269) SS BOND : bond 0.00353 / 0.18 ( 4) SS BOND : angle 0.38014 / 0.21 ( 8) hydrogen bonds : bond 0.03227 / 2.21 ( 547) hydrogen bonds : angle 3.45392 / 2.58 ( 1641) link_BETA1-4 : bond 0.00472 / 0.22 ( 8) link_BETA1-4 : angle 1.75828 / 1.24 ( 24) link_NAG-ASN : bond 0.00234 / 0.12 ( 4) link_NAG-ASN : angle 2.76244 / 1.81 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 971.48 seconds wall clock time: 17 minutes 33.71 seconds (1053.71 seconds total)