Starting phenix.real_space_refine on Tue Feb 3 19:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yb5_72749/02_2026/9yb5_72749.map" } resolution = 3.2 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= 0.007 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 4053 2.51 5 N 1088 2.21 5 O 1220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6402 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3573 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 27, 'TRANS': 430} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1672 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1128 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.54, per 1000 atoms: 0.24 Number of scatterers: 6402 At special positions: 0 Unit cell: (62.78, 98.55, 112.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 2 15.00 Mg 1 11.99 O 1220 8.00 N 1088 7.00 C 4053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 243.8 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 59.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 removed outlier: 4.387A pdb=" N ILE B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 32 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 107 through 121 removed outlier: 4.184A pdb=" N GLN B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.591A pdb=" N LEU B 166 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 167 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.629A pdb=" N ILE B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 301 removed outlier: 3.865A pdb=" N GLN B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 318 through 332 Proline residue: B 324 - end of helix removed outlier: 3.710A pdb=" N THR B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.586A pdb=" N ALA B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 375 removed outlier: 4.534A pdb=" N HIS B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Proline residue: B 369 - end of helix Processing helix chain 'B' and resid 379 through 393 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.792A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'D' and resid 25 through 32 removed outlier: 3.575A pdb=" N HIS D 30 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.817A pdb=" N TYR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.635A pdb=" N VAL D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 158 through 170 Processing helix chain 'D' and resid 190 through 207 Processing helix chain 'D' and resid 207 through 215 removed outlier: 4.213A pdb=" N ASP D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 160 removed outlier: 3.913A pdb=" N LYS C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 47 through 54 removed outlier: 6.437A pdb=" N PHE D 11 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP D 64 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU D 13 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS D 12 " --> pdb=" O CYS D 85 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 87 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL D 14 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 89 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN D 145 " --> pdb=" O ILE D 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.536A pdb=" N ALA C 92 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 83 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP C 66 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 47 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR C 64 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 45 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP C 66 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN C 43 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 68 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE C 41 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 70 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU C 39 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS C 72 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU C 37 " --> pdb=" O HIS C 72 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 129 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS C 126 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 118 " --> pdb=" O LYS C 126 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1014 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: 0.93 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: 1.23 - 1.34: 2131 1.34 - 1.46: 1298 1.46 - 1.58: 3043 1.58 - 1.69: 3 1.69 - 1.81: 56 Bond restraints: 6531 Sorted by residual: bond pdb=" CB PRO C 104 " pdb=" CG PRO C 104 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.18e+00 bond pdb=" C5 GDP D 302 " pdb=" C4 GDP D 302 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" N GLY B 304 " pdb=" CA GLY B 304 " ideal model delta sigma weight residual 1.449 1.462 -0.013 1.45e-02 4.76e+03 8.14e-01 bond pdb=" CB ARG C 110 " pdb=" CG ARG C 110 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.37e-01 bond pdb=" C LYS B 403 " pdb=" N PRO B 404 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 6.98e-01 ... (remaining 6526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 8661 1.42 - 2.85: 151 2.85 - 4.27: 35 4.27 - 5.70: 16 5.70 - 7.12: 2 Bond angle restraints: 8865 Sorted by residual: angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 112.96 110.71 2.25 1.00e+00 1.00e+00 5.06e+00 angle pdb=" CA ARG C 110 " pdb=" CB ARG C 110 " pdb=" CG ARG C 110 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.02e+00 angle pdb=" C GLU D 113 " pdb=" N ASN D 114 " pdb=" CA ASN D 114 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" N LYS B 403 " pdb=" CA LYS B 403 " pdb=" C LYS B 403 " ideal model delta sigma weight residual 109.81 114.38 -4.57 2.21e+00 2.05e-01 4.28e+00 angle pdb=" CA LEU B 439 " pdb=" CB LEU B 439 " pdb=" CG LEU B 439 " ideal model delta sigma weight residual 116.30 123.42 -7.12 3.50e+00 8.16e-02 4.14e+00 ... (remaining 8860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.77: 3936 28.77 - 57.55: 69 57.55 - 86.32: 3 86.32 - 115.10: 1 115.10 - 143.87: 1 Dihedral angle restraints: 4010 sinusoidal: 1644 harmonic: 2366 Sorted by residual: dihedral pdb=" O4' GDP D 302 " pdb=" C1' GDP D 302 " pdb=" N9 GDP D 302 " pdb=" C8 GDP D 302 " ideal model delta sinusoidal sigma weight residual 27.02 -116.85 143.87 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" CA GLU C 101 " pdb=" C GLU C 101 " pdb=" N LEU C 102 " pdb=" CA LEU C 102 " ideal model delta harmonic sigma weight residual 180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 134 " pdb=" C PHE C 134 " pdb=" N LEU C 135 " pdb=" CA LEU C 135 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 571 0.028 - 0.055: 276 0.055 - 0.083: 79 0.083 - 0.110: 66 0.110 - 0.138: 6 Chirality restraints: 998 Sorted by residual: chirality pdb=" CA LEU B 439 " pdb=" N LEU B 439 " pdb=" C LEU B 439 " pdb=" CB LEU B 439 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" C2' GDP D 302 " pdb=" C3' GDP D 302 " pdb=" O2' GDP D 302 " pdb=" C1' GDP D 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.64 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 995 not shown) Planarity restraints: 1151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 396 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO B 397 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 397 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 397 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 403 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 404 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 343 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 344 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.024 5.00e-02 4.00e+02 ... (remaining 1148 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 6 2.61 - 3.18: 5758 3.18 - 3.75: 9916 3.75 - 4.33: 13158 4.33 - 4.90: 22126 Nonbonded interactions: 50964 Sorted by model distance: nonbonded pdb="MG MG D 301 " pdb=" O2B GDP D 302 " model vdw 2.035 2.170 nonbonded pdb=" OG1 THR D 42 " pdb="MG MG D 301 " model vdw 2.064 2.170 nonbonded pdb="MG MG D 301 " pdb=" O1B GDP D 302 " model vdw 2.076 2.170 nonbonded pdb="MG MG D 301 " pdb=" PB GDP D 302 " model vdw 2.344 2.530 nonbonded pdb=" O3' GDP D 302 " pdb=" O2' GDP D 302 " model vdw 2.495 2.432 ... (remaining 50959 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.002 0.054 6531 Z= 0.107 Angle : 0.538 7.120 8865 Z= 0.276 Chirality : 0.040 0.138 998 Planarity : 0.005 0.056 1151 Dihedral : 11.225 143.869 2466 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 4.04 % Favored : 93.94 % 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: 1.58 (0.32), residues: 798 helix: 2.29 (0.26), residues: 437 sheet: 0.06 (0.58), residues: 82 loop : -0.68 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 133 TYR 0.006 0.001 TYR B 314 PHE 0.008 0.001 PHE C 50 TRP 0.010 0.001 TRP B 430 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6531) covalent geometry : angle 0.53763 ( 8865) hydrogen bonds : bond 0.14060 ( 344) hydrogen bonds : angle 5.27912 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 PHE cc_start: 0.9087 (t80) cc_final: 0.8860 (t80) REVERT: B 27 ARG cc_start: 0.9300 (mtp180) cc_final: 0.8932 (tpp80) REVERT: B 146 MET cc_start: 0.8721 (tpp) cc_final: 0.8315 (tpp) REVERT: B 168 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8847 (p0) REVERT: B 203 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9227 (tp30) REVERT: B 208 ASN cc_start: 0.9232 (m110) cc_final: 0.9024 (m-40) REVERT: B 216 HIS cc_start: 0.8869 (t-90) cc_final: 0.8401 (m90) REVERT: B 240 ASN cc_start: 0.9230 (m-40) cc_final: 0.8846 (m-40) REVERT: B 266 GLU cc_start: 0.8938 (tt0) cc_final: 0.8584 (tm-30) REVERT: B 274 GLU cc_start: 0.9090 (mp0) cc_final: 0.8763 (mp0) REVERT: B 339 ASP cc_start: 0.8986 (p0) cc_final: 0.8760 (t0) REVERT: B 388 MET cc_start: 0.9451 (tpt) cc_final: 0.8922 (tpp) REVERT: B 426 ASP cc_start: 0.9715 (m-30) cc_final: 0.9379 (p0) REVERT: D 36 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8200 (tp30) REVERT: D 56 ARG cc_start: 0.9444 (mmm-85) cc_final: 0.9206 (mmm-85) REVERT: D 91 ASP cc_start: 0.8222 (t0) cc_final: 0.7960 (t0) REVERT: D 112 CYS cc_start: 0.8670 (m) cc_final: 0.8325 (m) REVERT: D 154 ASN cc_start: 0.9407 (m110) cc_final: 0.9183 (m-40) REVERT: D 171 ASP cc_start: 0.8356 (t0) cc_final: 0.7469 (t0) REVERT: D 196 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9010 (tp-100) REVERT: D 200 ASP cc_start: 0.9582 (m-30) cc_final: 0.8864 (m-30) REVERT: C 32 THR cc_start: 0.9197 (p) cc_final: 0.8790 (p) REVERT: C 38 GLU cc_start: 0.9261 (tt0) cc_final: 0.8514 (mp0) REVERT: C 41 PHE cc_start: 0.8796 (t80) cc_final: 0.7786 (t80) REVERT: C 54 ASN cc_start: 0.8826 (t0) cc_final: 0.8419 (t0) REVERT: C 78 ILE cc_start: 0.9518 (tp) cc_final: 0.9230 (tp) REVERT: C 99 MET cc_start: 0.9183 (mpt) cc_final: 0.8943 (mpp) REVERT: C 154 ILE cc_start: 0.9652 (tp) cc_final: 0.9311 (tp) REVERT: C 157 ARG cc_start: 0.9433 (ttp80) cc_final: 0.9221 (ttp80) outliers start: 14 outliers final: 3 residues processed: 168 average time/residue: 0.0732 time to fit residues: 16.2490 Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN D 199 HIS C 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.085844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.057832 restraints weight = 16118.449| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.28 r_work: 0.2787 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6531 Z= 0.141 Angle : 0.602 7.626 8865 Z= 0.298 Chirality : 0.043 0.201 998 Planarity : 0.005 0.054 1151 Dihedral : 7.119 143.176 878 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.44 % Allowed : 10.68 % Favored : 87.88 % 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: 1.60 (0.32), residues: 798 helix: 2.28 (0.25), residues: 440 sheet: 0.54 (0.64), residues: 70 loop : -0.76 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.007 0.001 TYR D 146 PHE 0.013 0.001 PHE B 390 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6531) covalent geometry : angle 0.60178 ( 8865) hydrogen bonds : bond 0.03598 ( 344) hydrogen bonds : angle 4.31418 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9230 (mtp180) cc_final: 0.8886 (tpp80) REVERT: B 146 MET cc_start: 0.8827 (tpp) cc_final: 0.8443 (tpp) REVERT: B 203 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9230 (tp30) REVERT: B 208 ASN cc_start: 0.9075 (m110) cc_final: 0.8853 (m-40) REVERT: B 216 HIS cc_start: 0.8903 (t-90) cc_final: 0.8504 (m90) REVERT: B 240 ASN cc_start: 0.9258 (m-40) cc_final: 0.8846 (m110) REVERT: B 266 GLU cc_start: 0.8902 (tt0) cc_final: 0.8628 (tm-30) REVERT: B 274 GLU cc_start: 0.9161 (mp0) cc_final: 0.8781 (mp0) REVERT: B 339 ASP cc_start: 0.9202 (p0) cc_final: 0.8809 (t0) REVERT: B 388 MET cc_start: 0.9465 (tpt) cc_final: 0.8948 (tpp) REVERT: B 418 LYS cc_start: 0.9555 (tppt) cc_final: 0.9260 (mmtt) REVERT: B 426 ASP cc_start: 0.9681 (m-30) cc_final: 0.9360 (p0) REVERT: D 8 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8218 (mt0) REVERT: D 79 TYR cc_start: 0.9410 (m-80) cc_final: 0.8948 (m-80) REVERT: D 112 CYS cc_start: 0.8530 (m) cc_final: 0.8265 (m) REVERT: D 122 ASN cc_start: 0.9217 (t0) cc_final: 0.8999 (t0) REVERT: D 154 ASN cc_start: 0.9459 (m110) cc_final: 0.9253 (m-40) REVERT: D 171 ASP cc_start: 0.8380 (t0) cc_final: 0.7913 (t0) REVERT: D 196 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9219 (tp-100) REVERT: C 38 GLU cc_start: 0.9069 (tt0) cc_final: 0.8635 (mp0) REVERT: C 41 PHE cc_start: 0.8913 (t80) cc_final: 0.8336 (t80) REVERT: C 54 ASN cc_start: 0.8886 (t0) cc_final: 0.8445 (t0) REVERT: C 99 MET cc_start: 0.9142 (mpt) cc_final: 0.8936 (mpp) REVERT: C 109 ASP cc_start: 0.9248 (p0) cc_final: 0.9035 (p0) REVERT: C 154 ILE cc_start: 0.9686 (tp) cc_final: 0.9339 (tp) REVERT: C 157 ARG cc_start: 0.9402 (ttp80) cc_final: 0.9157 (ttp80) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.0893 time to fit residues: 15.7191 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS D 145 GLN D 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.059902 restraints weight = 15512.475| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.54 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6531 Z= 0.129 Angle : 0.592 6.766 8865 Z= 0.291 Chirality : 0.044 0.276 998 Planarity : 0.005 0.055 1151 Dihedral : 7.044 141.769 875 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.16 % Allowed : 11.26 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.32), residues: 798 helix: 2.21 (0.25), residues: 443 sheet: -0.33 (0.57), residues: 91 loop : -0.86 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.008 0.001 TYR D 146 PHE 0.019 0.001 PHE B 24 TRP 0.009 0.001 TRP B 430 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6531) covalent geometry : angle 0.59228 ( 8865) hydrogen bonds : bond 0.03414 ( 344) hydrogen bonds : angle 4.17751 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9090 (mtp180) cc_final: 0.8687 (tpp80) REVERT: B 146 MET cc_start: 0.8570 (tpp) cc_final: 0.8146 (tpp) REVERT: B 168 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8732 (p0) REVERT: B 182 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7728 (ttp-110) REVERT: B 203 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9064 (tp30) REVERT: B 208 ASN cc_start: 0.8717 (m110) cc_final: 0.8496 (m-40) REVERT: B 216 HIS cc_start: 0.8834 (t-90) cc_final: 0.8386 (m90) REVERT: B 240 ASN cc_start: 0.9101 (m-40) cc_final: 0.8669 (m110) REVERT: B 266 GLU cc_start: 0.8750 (tt0) cc_final: 0.8431 (tm-30) REVERT: B 274 GLU cc_start: 0.8924 (mp0) cc_final: 0.8424 (mp0) REVERT: B 339 ASP cc_start: 0.9103 (p0) cc_final: 0.8804 (t0) REVERT: B 377 ASN cc_start: 0.8085 (t0) cc_final: 0.7583 (t0) REVERT: B 388 MET cc_start: 0.9251 (tpt) cc_final: 0.8805 (tpp) REVERT: D 36 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7721 (tp30) REVERT: D 79 TYR cc_start: 0.9186 (m-80) cc_final: 0.8647 (m-80) REVERT: D 112 CYS cc_start: 0.7972 (m) cc_final: 0.7627 (m) REVERT: D 196 GLN cc_start: 0.9513 (tp-100) cc_final: 0.9290 (tp-100) REVERT: C 41 PHE cc_start: 0.8671 (t80) cc_final: 0.8065 (t80) REVERT: C 54 ASN cc_start: 0.8751 (t0) cc_final: 0.8397 (t0) REVERT: C 67 VAL cc_start: 0.8445 (t) cc_final: 0.8159 (m) REVERT: C 99 MET cc_start: 0.9167 (mpt) cc_final: 0.8957 (mpp) REVERT: C 109 ASP cc_start: 0.9312 (p0) cc_final: 0.9105 (p0) REVERT: C 117 HIS cc_start: 0.8421 (m-70) cc_final: 0.8055 (m-70) REVERT: C 154 ILE cc_start: 0.9590 (tp) cc_final: 0.9247 (tp) REVERT: C 157 ARG cc_start: 0.9416 (ttp80) cc_final: 0.9177 (ttp80) outliers start: 15 outliers final: 8 residues processed: 131 average time/residue: 0.0742 time to fit residues: 13.0279 Evaluate side-chains 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 309 HIS D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058411 restraints weight = 15955.266| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.65 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6531 Z= 0.166 Angle : 0.605 6.757 8865 Z= 0.300 Chirality : 0.043 0.236 998 Planarity : 0.005 0.055 1151 Dihedral : 7.127 143.516 875 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.02 % Allowed : 12.55 % Favored : 85.43 % 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: 1.44 (0.32), residues: 798 helix: 2.26 (0.25), residues: 444 sheet: -0.27 (0.57), residues: 87 loop : -0.87 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.008 0.001 TYR D 146 PHE 0.011 0.001 PHE B 24 TRP 0.008 0.001 TRP B 430 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6531) covalent geometry : angle 0.60465 ( 8865) hydrogen bonds : bond 0.03270 ( 344) hydrogen bonds : angle 4.17736 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8659 (tpp80) REVERT: B 168 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8687 (p0) REVERT: B 182 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7665 (ttp-110) REVERT: B 216 HIS cc_start: 0.8856 (t-90) cc_final: 0.8422 (m90) REVERT: B 240 ASN cc_start: 0.9125 (m-40) cc_final: 0.8663 (m110) REVERT: B 252 MET cc_start: 0.9626 (mmp) cc_final: 0.9405 (mmp) REVERT: B 266 GLU cc_start: 0.8773 (tt0) cc_final: 0.8469 (tm-30) REVERT: B 274 GLU cc_start: 0.8935 (mp0) cc_final: 0.8431 (mp0) REVERT: B 339 ASP cc_start: 0.9093 (p0) cc_final: 0.8813 (t0) REVERT: B 374 HIS cc_start: 0.8378 (m-70) cc_final: 0.7974 (m-70) REVERT: B 377 ASN cc_start: 0.8207 (t0) cc_final: 0.7592 (t0) REVERT: B 388 MET cc_start: 0.9262 (tpt) cc_final: 0.8814 (tpp) REVERT: D 8 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8235 (mt0) REVERT: D 112 CYS cc_start: 0.8054 (m) cc_final: 0.7688 (m) REVERT: D 196 GLN cc_start: 0.9589 (tp-100) cc_final: 0.9385 (tp-100) REVERT: D 197 TYR cc_start: 0.9257 (m-10) cc_final: 0.8827 (m-10) REVERT: C 41 PHE cc_start: 0.8599 (t80) cc_final: 0.8240 (t80) REVERT: C 54 ASN cc_start: 0.8747 (t0) cc_final: 0.8387 (t0) REVERT: C 99 MET cc_start: 0.9152 (mpt) cc_final: 0.8943 (mpp) REVERT: C 109 ASP cc_start: 0.9320 (p0) cc_final: 0.9118 (p0) REVERT: C 117 HIS cc_start: 0.8408 (m-70) cc_final: 0.7972 (m-70) REVERT: C 154 ILE cc_start: 0.9612 (tp) cc_final: 0.9263 (tp) REVERT: C 157 ARG cc_start: 0.9423 (ttp80) cc_final: 0.9159 (ttp80) outliers start: 14 outliers final: 9 residues processed: 120 average time/residue: 0.0715 time to fit residues: 11.6311 Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN D 145 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.059118 restraints weight = 15907.873| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.52 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6531 Z= 0.138 Angle : 0.611 10.805 8865 Z= 0.298 Chirality : 0.043 0.255 998 Planarity : 0.005 0.055 1151 Dihedral : 7.126 143.715 875 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 12.99 % Favored : 85.28 % 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: 1.52 (0.31), residues: 798 helix: 2.28 (0.25), residues: 443 sheet: -0.07 (0.58), residues: 85 loop : -0.81 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 133 TYR 0.010 0.001 TYR D 146 PHE 0.007 0.001 PHE D 61 TRP 0.008 0.001 TRP B 430 HIS 0.008 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6531) covalent geometry : angle 0.61104 ( 8865) hydrogen bonds : bond 0.03144 ( 344) hydrogen bonds : angle 4.12308 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9090 (mtp180) cc_final: 0.8637 (tpp80) REVERT: B 146 MET cc_start: 0.8574 (tpp) cc_final: 0.8332 (tpp) REVERT: B 168 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (p0) REVERT: B 182 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7662 (ttp-110) REVERT: B 208 ASN cc_start: 0.8612 (m110) cc_final: 0.8174 (t0) REVERT: B 216 HIS cc_start: 0.8853 (t-90) cc_final: 0.8426 (m90) REVERT: B 240 ASN cc_start: 0.9109 (m-40) cc_final: 0.8653 (m110) REVERT: B 252 MET cc_start: 0.9624 (mmp) cc_final: 0.9394 (mmp) REVERT: B 266 GLU cc_start: 0.8762 (tt0) cc_final: 0.8452 (tm-30) REVERT: B 274 GLU cc_start: 0.8919 (mp0) cc_final: 0.8411 (mp0) REVERT: B 339 ASP cc_start: 0.9085 (p0) cc_final: 0.8816 (t0) REVERT: B 374 HIS cc_start: 0.8385 (m-70) cc_final: 0.7955 (m-70) REVERT: B 377 ASN cc_start: 0.8234 (t0) cc_final: 0.7619 (t0) REVERT: B 388 MET cc_start: 0.9264 (tpt) cc_final: 0.8818 (tpp) REVERT: D 8 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8150 (mt0) REVERT: D 10 GLN cc_start: 0.8909 (pm20) cc_final: 0.8270 (pt0) REVERT: D 36 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7739 (tp30) REVERT: D 112 CYS cc_start: 0.8026 (m) cc_final: 0.7641 (m) REVERT: D 197 TYR cc_start: 0.9259 (m-10) cc_final: 0.8789 (m-10) REVERT: C 36 ASP cc_start: 0.9088 (m-30) cc_final: 0.8528 (t0) REVERT: C 41 PHE cc_start: 0.8543 (t80) cc_final: 0.8273 (t80) REVERT: C 54 ASN cc_start: 0.8865 (t0) cc_final: 0.8376 (t0) REVERT: C 109 ASP cc_start: 0.9303 (p0) cc_final: 0.9096 (p0) REVERT: C 117 HIS cc_start: 0.8408 (m-70) cc_final: 0.8010 (m-70) REVERT: C 154 ILE cc_start: 0.9615 (tp) cc_final: 0.9274 (tp) REVERT: C 157 ARG cc_start: 0.9420 (ttp80) cc_final: 0.9154 (ttp80) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.0627 time to fit residues: 10.6074 Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.057387 restraints weight = 15953.560| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.59 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6531 Z= 0.166 Angle : 0.636 12.374 8865 Z= 0.310 Chirality : 0.044 0.260 998 Planarity : 0.005 0.055 1151 Dihedral : 7.193 145.659 875 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.16 % Allowed : 13.28 % Favored : 84.56 % 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: 1.54 (0.31), residues: 798 helix: 2.36 (0.25), residues: 440 sheet: -0.14 (0.58), residues: 85 loop : -0.85 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 133 TYR 0.010 0.001 TYR D 146 PHE 0.008 0.001 PHE D 61 TRP 0.007 0.001 TRP B 430 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6531) covalent geometry : angle 0.63638 ( 8865) hydrogen bonds : bond 0.03222 ( 344) hydrogen bonds : angle 4.13573 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8628 (tpp80) REVERT: B 146 MET cc_start: 0.8583 (tpp) cc_final: 0.8329 (tpp) REVERT: B 168 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8692 (p0) REVERT: B 182 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7648 (ttp-110) REVERT: B 208 ASN cc_start: 0.8720 (m110) cc_final: 0.8344 (t0) REVERT: B 216 HIS cc_start: 0.8865 (t-90) cc_final: 0.8464 (m-70) REVERT: B 240 ASN cc_start: 0.9121 (m-40) cc_final: 0.8666 (m110) REVERT: B 252 MET cc_start: 0.9647 (mmp) cc_final: 0.9411 (mmp) REVERT: B 266 GLU cc_start: 0.8760 (tt0) cc_final: 0.8449 (tm-30) REVERT: B 274 GLU cc_start: 0.8924 (mp0) cc_final: 0.8412 (mp0) REVERT: B 339 ASP cc_start: 0.9081 (p0) cc_final: 0.8834 (t0) REVERT: B 377 ASN cc_start: 0.8215 (t0) cc_final: 0.7712 (t0) REVERT: B 388 MET cc_start: 0.9254 (tpt) cc_final: 0.8812 (tpp) REVERT: D 76 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: D 112 CYS cc_start: 0.8045 (m) cc_final: 0.7665 (m) REVERT: D 167 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9167 (tppp) REVERT: D 197 TYR cc_start: 0.9278 (m-10) cc_final: 0.8857 (m-10) REVERT: C 36 ASP cc_start: 0.9163 (m-30) cc_final: 0.8551 (t0) REVERT: C 54 ASN cc_start: 0.8886 (t0) cc_final: 0.8367 (t0) REVERT: C 117 HIS cc_start: 0.8372 (m-70) cc_final: 0.8107 (m90) REVERT: C 154 ILE cc_start: 0.9606 (tp) cc_final: 0.9269 (tp) REVERT: C 157 ARG cc_start: 0.9426 (ttp80) cc_final: 0.9151 (ttp80) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.0696 time to fit residues: 11.6622 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.088623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060719 restraints weight = 15619.469| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.51 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6531 Z= 0.114 Angle : 0.628 13.053 8865 Z= 0.303 Chirality : 0.043 0.275 998 Planarity : 0.005 0.056 1151 Dihedral : 7.118 143.617 875 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 14.29 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.31), residues: 798 helix: 2.30 (0.25), residues: 442 sheet: -0.23 (0.58), residues: 85 loop : -0.81 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.010 0.001 TYR D 146 PHE 0.007 0.001 PHE D 61 TRP 0.008 0.001 TRP B 430 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6531) covalent geometry : angle 0.62799 ( 8865) hydrogen bonds : bond 0.02846 ( 344) hydrogen bonds : angle 3.98944 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9084 (mtp180) cc_final: 0.8604 (tpp80) REVERT: B 146 MET cc_start: 0.8551 (tpp) cc_final: 0.8294 (tpp) REVERT: B 168 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8748 (p0) REVERT: B 182 ARG cc_start: 0.7952 (ptm160) cc_final: 0.7677 (ttp-110) REVERT: B 208 ASN cc_start: 0.8724 (m110) cc_final: 0.8324 (t0) REVERT: B 216 HIS cc_start: 0.8840 (t-90) cc_final: 0.8439 (m90) REVERT: B 240 ASN cc_start: 0.9063 (m-40) cc_final: 0.8669 (m110) REVERT: B 252 MET cc_start: 0.9590 (mmp) cc_final: 0.9382 (mmp) REVERT: B 266 GLU cc_start: 0.8750 (tt0) cc_final: 0.8435 (tm-30) REVERT: B 274 GLU cc_start: 0.8892 (mp0) cc_final: 0.8389 (mp0) REVERT: B 339 ASP cc_start: 0.9075 (p0) cc_final: 0.8827 (t0) REVERT: B 374 HIS cc_start: 0.8462 (m-70) cc_final: 0.8103 (m-70) REVERT: B 377 ASN cc_start: 0.8346 (t0) cc_final: 0.7750 (t0) REVERT: B 388 MET cc_start: 0.9277 (tpt) cc_final: 0.8829 (tpp) REVERT: D 8 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8555 (mt0) REVERT: D 10 GLN cc_start: 0.8885 (pm20) cc_final: 0.8321 (pt0) REVERT: D 36 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7680 (tp30) REVERT: D 76 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.8026 (mmm-85) REVERT: D 112 CYS cc_start: 0.7995 (m) cc_final: 0.7611 (m) REVERT: D 167 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9171 (tppp) REVERT: D 197 TYR cc_start: 0.9297 (m-10) cc_final: 0.8716 (m-80) REVERT: C 36 ASP cc_start: 0.9160 (m-30) cc_final: 0.8555 (t0) REVERT: C 54 ASN cc_start: 0.9000 (t0) cc_final: 0.8548 (t0) REVERT: C 117 HIS cc_start: 0.8319 (m-70) cc_final: 0.7976 (m-70) REVERT: C 154 ILE cc_start: 0.9626 (tp) cc_final: 0.9282 (tp) REVERT: C 157 ARG cc_start: 0.9398 (ttp80) cc_final: 0.9105 (ttp80) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.0681 time to fit residues: 11.7968 Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.087980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.060259 restraints weight = 15441.432| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.43 r_work: 0.2667 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6531 Z= 0.127 Angle : 0.632 12.366 8865 Z= 0.307 Chirality : 0.043 0.291 998 Planarity : 0.005 0.055 1151 Dihedral : 7.121 144.898 875 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.73 % Allowed : 14.57 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.31), residues: 798 helix: 2.33 (0.25), residues: 443 sheet: -0.00 (0.59), residues: 76 loop : -0.88 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 133 TYR 0.012 0.001 TYR D 155 PHE 0.008 0.001 PHE C 147 TRP 0.008 0.001 TRP B 430 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6531) covalent geometry : angle 0.63244 ( 8865) hydrogen bonds : bond 0.02883 ( 344) hydrogen bonds : angle 3.99482 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9178 (mtp180) cc_final: 0.8707 (tpp80) REVERT: B 146 MET cc_start: 0.8681 (tpp) cc_final: 0.8448 (tpp) REVERT: B 168 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8873 (p0) REVERT: B 182 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7926 (tmm-80) REVERT: B 208 ASN cc_start: 0.8878 (m110) cc_final: 0.8473 (t0) REVERT: B 216 HIS cc_start: 0.8863 (t-90) cc_final: 0.8466 (m-70) REVERT: B 240 ASN cc_start: 0.9195 (m-40) cc_final: 0.8751 (m110) REVERT: B 266 GLU cc_start: 0.8934 (tt0) cc_final: 0.8596 (tm-30) REVERT: B 274 GLU cc_start: 0.9038 (mp0) cc_final: 0.8627 (mp0) REVERT: B 339 ASP cc_start: 0.9161 (p0) cc_final: 0.8867 (t0) REVERT: B 374 HIS cc_start: 0.8537 (m-70) cc_final: 0.8177 (m-70) REVERT: B 377 ASN cc_start: 0.8466 (t0) cc_final: 0.7899 (t0) REVERT: B 388 MET cc_start: 0.9242 (tpt) cc_final: 0.8838 (tpp) REVERT: D 8 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8517 (mt0) REVERT: D 10 GLN cc_start: 0.8970 (pm20) cc_final: 0.8368 (pt0) REVERT: D 36 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7932 (tp30) REVERT: D 76 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8332 (mmm-85) REVERT: D 112 CYS cc_start: 0.8299 (m) cc_final: 0.7935 (m) REVERT: D 167 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9199 (tppp) REVERT: D 197 TYR cc_start: 0.9284 (m-10) cc_final: 0.8731 (m-80) REVERT: C 36 ASP cc_start: 0.9194 (m-30) cc_final: 0.8592 (t0) REVERT: C 54 ASN cc_start: 0.9105 (t0) cc_final: 0.8661 (t0) REVERT: C 117 HIS cc_start: 0.8607 (m-70) cc_final: 0.8311 (m-70) REVERT: C 154 ILE cc_start: 0.9632 (tp) cc_final: 0.9291 (tp) REVERT: C 157 ARG cc_start: 0.9420 (ttp80) cc_final: 0.9123 (ttp80) outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 0.0657 time to fit residues: 10.8187 Evaluate side-chains 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 129 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.087280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.058791 restraints weight = 16075.153| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.61 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6531 Z= 0.153 Angle : 0.656 12.259 8865 Z= 0.319 Chirality : 0.044 0.311 998 Planarity : 0.005 0.055 1151 Dihedral : 7.186 146.636 875 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.59 % Allowed : 14.86 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.31), residues: 798 helix: 2.34 (0.25), residues: 443 sheet: -0.33 (0.57), residues: 85 loop : -0.75 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 110 TYR 0.009 0.001 TYR D 146 PHE 0.016 0.001 PHE B 390 TRP 0.006 0.001 TRP B 430 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6531) covalent geometry : angle 0.65583 ( 8865) hydrogen bonds : bond 0.02976 ( 344) hydrogen bonds : angle 4.05529 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.304 Fit side-chains REVERT: B 27 ARG cc_start: 0.9098 (mtp180) cc_final: 0.8594 (tpp80) REVERT: B 146 MET cc_start: 0.8588 (tpp) cc_final: 0.8316 (tpp) REVERT: B 168 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8651 (p0) REVERT: B 182 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7564 (ttp-110) REVERT: B 208 ASN cc_start: 0.8756 (m110) cc_final: 0.8336 (t0) REVERT: B 216 HIS cc_start: 0.8858 (t-90) cc_final: 0.8482 (m-70) REVERT: B 240 ASN cc_start: 0.9107 (m-40) cc_final: 0.8643 (m110) REVERT: B 266 GLU cc_start: 0.8764 (tt0) cc_final: 0.8456 (tm-30) REVERT: B 274 GLU cc_start: 0.8908 (mp0) cc_final: 0.8397 (mp0) REVERT: B 339 ASP cc_start: 0.9080 (p0) cc_final: 0.8868 (t0) REVERT: B 374 HIS cc_start: 0.8588 (m-70) cc_final: 0.8227 (m-70) REVERT: B 377 ASN cc_start: 0.8346 (t0) cc_final: 0.7779 (t0) REVERT: B 388 MET cc_start: 0.9253 (tpt) cc_final: 0.8827 (tpp) REVERT: D 8 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8224 (mt0) REVERT: D 10 GLN cc_start: 0.8922 (pm20) cc_final: 0.8309 (pt0) REVERT: D 36 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7669 (tp30) REVERT: D 112 CYS cc_start: 0.8066 (m) cc_final: 0.7672 (m) REVERT: D 167 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9177 (tppp) REVERT: D 197 TYR cc_start: 0.9334 (m-10) cc_final: 0.8843 (m-10) REVERT: C 36 ASP cc_start: 0.9199 (m-30) cc_final: 0.8550 (t0) REVERT: C 54 ASN cc_start: 0.9112 (t0) cc_final: 0.8717 (t0) REVERT: C 117 HIS cc_start: 0.8307 (m-70) cc_final: 0.7983 (m-70) REVERT: C 154 ILE cc_start: 0.9631 (tp) cc_final: 0.9290 (tp) REVERT: C 157 ARG cc_start: 0.9403 (ttp80) cc_final: 0.9097 (ttp80) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.0637 time to fit residues: 10.4397 Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.059814 restraints weight = 15439.194| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.41 r_work: 0.2662 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6531 Z= 0.134 Angle : 0.657 13.221 8865 Z= 0.320 Chirality : 0.044 0.317 998 Planarity : 0.005 0.055 1151 Dihedral : 7.165 146.137 875 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 15.15 % Favored : 83.12 % 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: 1.51 (0.31), residues: 798 helix: 2.33 (0.25), residues: 443 sheet: -0.41 (0.57), residues: 85 loop : -0.78 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 305 TYR 0.010 0.001 TYR D 146 PHE 0.011 0.001 PHE B 390 TRP 0.007 0.001 TRP B 430 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6531) covalent geometry : angle 0.65729 ( 8865) hydrogen bonds : bond 0.02870 ( 344) hydrogen bonds : angle 4.03220 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 27 ARG cc_start: 0.9185 (mtp180) cc_final: 0.8713 (tpp80) REVERT: B 146 MET cc_start: 0.8685 (tpp) cc_final: 0.8448 (tpp) REVERT: B 168 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8879 (p0) REVERT: B 208 ASN cc_start: 0.8877 (m110) cc_final: 0.8461 (t0) REVERT: B 216 HIS cc_start: 0.8861 (t-90) cc_final: 0.8467 (m-70) REVERT: B 240 ASN cc_start: 0.9199 (m-40) cc_final: 0.8754 (m110) REVERT: B 266 GLU cc_start: 0.8938 (tt0) cc_final: 0.8599 (tm-30) REVERT: B 274 GLU cc_start: 0.9022 (mp0) cc_final: 0.8651 (mp0) REVERT: B 339 ASP cc_start: 0.9176 (p0) cc_final: 0.8897 (t0) REVERT: B 374 HIS cc_start: 0.8562 (m-70) cc_final: 0.8203 (m-70) REVERT: B 377 ASN cc_start: 0.8502 (t0) cc_final: 0.7967 (t0) REVERT: B 388 MET cc_start: 0.9237 (tpt) cc_final: 0.8841 (tpp) REVERT: D 10 GLN cc_start: 0.8985 (pm20) cc_final: 0.8403 (pt0) REVERT: D 36 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7901 (tp30) REVERT: D 112 CYS cc_start: 0.8302 (m) cc_final: 0.7920 (m) REVERT: D 167 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9185 (tppp) REVERT: D 197 TYR cc_start: 0.9314 (m-10) cc_final: 0.8820 (m-10) REVERT: C 36 ASP cc_start: 0.9226 (m-30) cc_final: 0.8590 (t0) REVERT: C 41 PHE cc_start: 0.8093 (t80) cc_final: 0.7855 (t80) REVERT: C 54 ASN cc_start: 0.9175 (t0) cc_final: 0.8769 (t0) REVERT: C 117 HIS cc_start: 0.8654 (m-70) cc_final: 0.8324 (m-70) REVERT: C 154 ILE cc_start: 0.9637 (tp) cc_final: 0.9297 (tp) REVERT: C 157 ARG cc_start: 0.9427 (ttp80) cc_final: 0.9113 (ttp80) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.0723 time to fit residues: 11.7759 Evaluate side-chains 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.087417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.059831 restraints weight = 15594.459| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.42 r_work: 0.2662 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6531 Z= 0.163 Angle : 1.047 59.200 8865 Z= 0.583 Chirality : 0.045 0.305 998 Planarity : 0.005 0.055 1151 Dihedral : 7.171 146.133 875 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.59 % Allowed : 16.02 % Favored : 82.40 % Cbeta Deviations : 0.13 % 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: 1.50 (0.31), residues: 798 helix: 2.31 (0.25), residues: 443 sheet: -0.40 (0.57), residues: 85 loop : -0.78 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.007 0.001 TYR D 80 PHE 0.010 0.001 PHE B 390 TRP 0.007 0.001 TRP B 430 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6531) covalent geometry : angle 1.04711 ( 8865) hydrogen bonds : bond 0.02854 ( 344) hydrogen bonds : angle 4.11607 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.98 seconds wall clock time: 23 minutes 35.88 seconds (1415.88 seconds total)