Starting phenix.real_space_refine on Tue Feb 11 11:37:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.map" model { file = "/net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a01_15044/02_2025/8a01_15044.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.76, per 1000 atoms: 0.68 Number of scatterers: 5511 At special positions: 0 Unit cell: (104.16, 97.96, 71.92, 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 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.24 Conformation dependent library (CDL) restraints added in 709.4 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.2% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.514A pdb=" N SER C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.652A pdb=" N LEU B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.638A pdb=" N SER B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 7 removed outlier: 5.422A pdb=" N LYS C 2 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 119 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 23 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 17 removed outlier: 3.557A pdb=" N SER C 101 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 40 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN C 56 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 42 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 136 removed outlier: 5.664A pdb=" N ASN C 230 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 153 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.570A pdb=" N GLN C 168 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 219 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER C 166 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE C 221 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 164 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 223 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 162 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.711A pdb=" N LEU B 117 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 5 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 115 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG B 114 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 28 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 116 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 26 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS B 118 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 24 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 120 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 7.237A pdb=" N ILE B 40 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 56 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 42 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.260A pdb=" N SER B 93 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 137 removed outlier: 5.983A pdb=" N ASN B 230 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 157 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 153 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.457A pdb=" N GLN B 168 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 219 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 166 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 221 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 164 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 223 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 162 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.584A pdb=" N LYS A 2 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 4 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 27 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 17 removed outlier: 7.006A pdb=" N ILE A 40 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A 56 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 42 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.757A pdb=" N SER A 93 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 137 removed outlier: 5.535A pdb=" N ASN A 230 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 153 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.525A pdb=" N GLN A 168 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 219 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 166 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 221 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 164 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 223 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 162 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 194 through 195 201 hydrogen bonds defined for protein. 531 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: 1.55 Time building geometry restraints manager: 1.47 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: 1818 1.34 - 1.46: 1045 1.46 - 1.58: 2684 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " ideal model delta sigma weight residual 1.536 1.553 -0.017 2.08e-02 2.31e+03 6.77e-01 bond pdb=" CB ASP C 29 " pdb=" CG ASP C 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.77e-01 bond pdb=" CA ASN B 143 " pdb=" CB ASN B 143 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.76e-02 3.23e+03 4.52e-01 bond pdb=" CB ASN B 143 " pdb=" CG ASN B 143 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.19e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 7178 0.86 - 1.72: 297 1.72 - 2.58: 46 2.58 - 3.44: 20 3.44 - 4.30: 7 Bond angle restraints: 7548 Sorted by residual: angle pdb=" N LYS C 223 " pdb=" CA LYS C 223 " pdb=" C LYS C 223 " ideal model delta sigma weight residual 108.34 111.92 -3.58 1.31e+00 5.83e-01 7.46e+00 angle pdb=" C ALA C 138 " pdb=" N SER C 139 " pdb=" CA SER C 139 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.07e+00 angle pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 112.60 114.26 -1.66 1.00e+00 1.00e+00 2.75e+00 angle pdb=" C ILE C 3 " pdb=" N ALA C 4 " pdb=" CA ALA C 4 " ideal model delta sigma weight residual 121.62 118.94 2.68 1.83e+00 2.99e-01 2.14e+00 angle pdb=" CA TYR B 167 " pdb=" CB TYR B 167 " pdb=" CG TYR B 167 " ideal model delta sigma weight residual 113.90 116.48 -2.58 1.80e+00 3.09e-01 2.05e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3068 17.43 - 34.86: 270 34.86 - 52.29: 60 52.29 - 69.73: 13 69.73 - 87.16: 9 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " pdb=" CD LYS A 57 " pdb=" CE LYS A 57 " ideal model delta sinusoidal sigma weight residual -180.00 -126.25 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CB LYS B 200 " pdb=" CG LYS B 200 " pdb=" CD LYS B 200 " pdb=" CE LYS B 200 " ideal model delta sinusoidal sigma weight residual 60.00 112.52 -52.52 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CB GLU B 141 " pdb=" CG GLU B 141 " pdb=" CD GLU B 141 " pdb=" OE1 GLU B 141 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 564 0.027 - 0.054: 188 0.054 - 0.081: 71 0.081 - 0.109: 72 0.109 - 0.136: 41 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 221 " pdb=" N ILE C 221 " pdb=" C ILE C 221 " pdb=" CB ILE C 221 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 178 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.03e-01 pdb=" N PRO B 179 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO C 179 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.67e-01 pdb=" N PRO A 212 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1470 2.81 - 3.33: 4379 3.33 - 3.86: 8347 3.86 - 4.38: 9858 4.38 - 4.90: 18283 Nonbonded interactions: 42337 Sorted by model distance: nonbonded pdb=" OG SER C 163 " pdb=" O ASN C 222 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 64 " pdb=" OG1 THR A 68 " model vdw 2.297 3.040 nonbonded pdb=" NE2 GLN B 183 " pdb=" OD2 ASP A 77 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASN B 128 " pdb=" OG1 THR B 238 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASP C 98 " pdb=" N LYS C 99 " model vdw 2.375 3.120 ... (remaining 42332 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.600 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 0.021 5571 Z= 0.118 Angle : 0.437 4.302 7548 Z= 0.240 Chirality : 0.046 0.136 936 Planarity : 0.002 0.024 960 Dihedral : 14.812 87.157 2064 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 711 helix: 1.53 (0.67), residues: 63 sheet: 0.94 (0.31), residues: 282 loop : -1.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 118 PHE 0.006 0.001 PHE A 231 TYR 0.010 0.001 TYR C 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.686 Fit side-chains REVERT: C 171 ASN cc_start: 0.8580 (p0) cc_final: 0.8301 (p0) REVERT: A 149 GLN cc_start: 0.7674 (tt0) cc_final: 0.7446 (tt0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1648 time to fit residues: 25.3639 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 203 GLN B 149 GLN B 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096340 restraints weight = 7472.787| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.75 r_work: 0.2884 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 5571 Z= 0.448 Angle : 0.612 4.988 7548 Z= 0.328 Chirality : 0.052 0.156 936 Planarity : 0.004 0.027 960 Dihedral : 4.702 18.325 750 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.59 % Allowed : 9.05 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.31), residues: 711 helix: 0.91 (0.65), residues: 63 sheet: 0.63 (0.31), residues: 291 loop : -1.16 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.013 0.002 PHE B 231 TYR 0.015 0.002 TYR C 43 ARG 0.002 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.692 Fit side-chains REVERT: C 100 GLU cc_start: 0.8327 (mp0) cc_final: 0.8016 (mp0) REVERT: B 87 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: A 149 GLN cc_start: 0.8216 (tt0) cc_final: 0.7993 (tt0) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1775 time to fit residues: 22.3619 Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100707 restraints weight = 7360.980| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.78 r_work: 0.2957 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 5571 Z= 0.130 Angle : 0.427 3.631 7548 Z= 0.238 Chirality : 0.046 0.134 936 Planarity : 0.003 0.027 960 Dihedral : 3.977 13.508 750 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.11 % Allowed : 11.90 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 711 helix: 1.39 (0.67), residues: 63 sheet: 0.95 (0.32), residues: 276 loop : -1.11 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 118 PHE 0.008 0.001 PHE B 231 TYR 0.011 0.001 TYR B 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.654 Fit side-chains REVERT: C 19 LYS cc_start: 0.8369 (ptpt) cc_final: 0.8119 (pttt) REVERT: C 100 GLU cc_start: 0.8137 (mp0) cc_final: 0.7749 (mp0) REVERT: B 87 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6648 (pm20) outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.1769 time to fit residues: 23.5094 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 230 ASN B 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.097085 restraints weight = 7523.723| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.79 r_work: 0.2889 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5571 Z= 0.321 Angle : 0.523 4.029 7548 Z= 0.284 Chirality : 0.049 0.146 936 Planarity : 0.003 0.027 960 Dihedral : 4.425 16.181 750 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 711 helix: 1.31 (0.68), residues: 63 sheet: 0.45 (0.30), residues: 321 loop : -1.26 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.014 0.001 TYR B 43 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.625 Fit side-chains REVERT: C 19 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8192 (pttt) REVERT: B 87 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6877 (pm20) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 0.1782 time to fit residues: 22.1244 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098017 restraints weight = 7425.523| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.78 r_work: 0.2903 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5571 Z= 0.229 Angle : 0.476 3.916 7548 Z= 0.263 Chirality : 0.047 0.142 936 Planarity : 0.003 0.027 960 Dihedral : 4.274 15.547 750 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.90 % Allowed : 15.56 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 711 helix: 1.37 (0.68), residues: 63 sheet: 0.40 (0.30), residues: 321 loop : -1.23 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.010 0.001 PHE B 231 TYR 0.013 0.001 TYR B 43 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.612 Fit side-chains REVERT: C 19 LYS cc_start: 0.8470 (ptpt) cc_final: 0.8180 (pttt) REVERT: C 100 GLU cc_start: 0.8209 (mp0) cc_final: 0.7853 (mp0) REVERT: B 87 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6861 (pm20) REVERT: B 156 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8671 (ptm) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.1763 time to fit residues: 22.0441 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095124 restraints weight = 7495.972| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.80 r_work: 0.2864 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5571 Z= 0.417 Angle : 0.582 4.512 7548 Z= 0.314 Chirality : 0.050 0.147 936 Planarity : 0.003 0.028 960 Dihedral : 4.751 18.123 750 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.86 % Allowed : 16.03 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.30), residues: 711 helix: 1.14 (0.67), residues: 63 sheet: 0.42 (0.31), residues: 288 loop : -1.29 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.010 0.002 PHE B 231 TYR 0.016 0.002 TYR B 43 ARG 0.003 0.001 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.636 Fit side-chains REVERT: B 87 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6809 (pm20) REVERT: A 48 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8627 (m110) outliers start: 18 outliers final: 12 residues processed: 95 average time/residue: 0.1719 time to fit residues: 21.5043 Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.108825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.096576 restraints weight = 7480.166| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.79 r_work: 0.2882 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5571 Z= 0.292 Angle : 0.516 4.140 7548 Z= 0.282 Chirality : 0.048 0.143 936 Planarity : 0.003 0.029 960 Dihedral : 4.511 16.955 750 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 711 helix: 1.21 (0.67), residues: 63 sheet: 0.42 (0.31), residues: 288 loop : -1.24 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.015 0.001 TYR B 43 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.599 Fit side-chains REVERT: C 100 GLU cc_start: 0.8298 (mp0) cc_final: 0.7979 (mp0) REVERT: B 87 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: B 156 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8619 (ptm) REVERT: A 48 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8533 (m110) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.1709 time to fit residues: 21.2784 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 0.0770 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.095485 restraints weight = 7469.045| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.81 r_work: 0.2870 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5571 Z= 0.351 Angle : 0.550 4.320 7548 Z= 0.298 Chirality : 0.049 0.144 936 Planarity : 0.003 0.029 960 Dihedral : 4.629 17.934 750 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.70 % Allowed : 17.14 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.30), residues: 711 helix: 1.15 (0.67), residues: 63 sheet: 0.31 (0.31), residues: 288 loop : -1.31 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.002 PHE B 231 TYR 0.015 0.002 TYR B 43 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.703 Fit side-chains REVERT: C 100 GLU cc_start: 0.8331 (mp0) cc_final: 0.7971 (mp0) REVERT: B 87 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6702 (pm20) REVERT: B 156 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: A 48 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8653 (m110) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.1725 time to fit residues: 21.0677 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096383 restraints weight = 7478.380| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.78 r_work: 0.2881 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5571 Z= 0.291 Angle : 0.516 4.178 7548 Z= 0.282 Chirality : 0.048 0.144 936 Planarity : 0.003 0.029 960 Dihedral : 4.514 17.250 750 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 17.46 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.31), residues: 711 helix: 1.19 (0.67), residues: 63 sheet: 0.32 (0.31), residues: 288 loop : -1.25 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.015 0.001 TYR B 43 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.666 Fit side-chains REVERT: C 100 GLU cc_start: 0.8324 (mp0) cc_final: 0.7973 (mp0) REVERT: B 87 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: B 156 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8632 (ptm) REVERT: A 48 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8511 (m110) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.1679 time to fit residues: 21.3019 Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.097563 restraints weight = 7448.960| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.78 r_work: 0.2900 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5571 Z= 0.225 Angle : 0.484 4.056 7548 Z= 0.266 Chirality : 0.048 0.143 936 Planarity : 0.003 0.029 960 Dihedral : 4.308 16.261 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.31), residues: 711 helix: 1.28 (0.68), residues: 63 sheet: 0.58 (0.31), residues: 273 loop : -1.27 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.014 0.001 TYR B 43 ARG 0.002 0.000 ARG C 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.598 Fit side-chains REVERT: C 100 GLU cc_start: 0.8234 (mp0) cc_final: 0.7884 (mp0) REVERT: C 141 GLU cc_start: 0.8315 (pt0) cc_final: 0.8052 (pt0) REVERT: B 87 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: B 156 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8620 (ptm) REVERT: A 48 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8521 (m110) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1578 time to fit residues: 19.6175 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096799 restraints weight = 7476.044| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.79 r_work: 0.2886 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5571 Z= 0.273 Angle : 0.509 4.162 7548 Z= 0.278 Chirality : 0.048 0.143 936 Planarity : 0.003 0.029 960 Dihedral : 4.403 16.913 750 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.31), residues: 711 helix: 1.24 (0.67), residues: 63 sheet: 0.37 (0.31), residues: 288 loop : -1.18 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.015 0.001 TYR B 43 ARG 0.003 0.000 ARG C 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.64 seconds wall clock time: 46 minutes 54.43 seconds (2814.43 seconds total)