Starting phenix.real_space_refine on Sat Aug 23 19:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zll_60228/08_2025/8zll_60228.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.104 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: 5 Type Number sf(0) Gaussians S 33 5.16 5 C 4515 2.51 5 N 1131 2.21 5 O 1197 1.98 5 H 6867 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13743 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4553 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 4.05, per 1000 atoms: 0.29 Number of scatterers: 13743 At special positions: 0 Unit cell: (83.7, 78.12, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 O 1197 8.00 N 1131 7.00 C 4515 6.00 H 6867 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.00 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.00 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " distance=2.00 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: 0.98 Conformation dependent library (CDL) restraints added in 286.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 33.9% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 61 through 98 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.602A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.873A pdb=" N SER A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 338 Processing helix chain 'B' and resid 62 through 98 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.602A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.873A pdb=" N SER B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 338 Processing helix chain 'C' and resid 62 through 98 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.601A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.873A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.118A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.118A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.556A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.118A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1191 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: 2.79 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6655 1.03 - 1.23: 243 1.23 - 1.42: 2939 1.42 - 1.61: 4035 1.61 - 1.81: 54 Bond restraints: 13926 Sorted by residual: bond pdb=" N CYS A 128 " pdb=" H CYS A 128 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N ASN B 155 " pdb=" H ASN B 155 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N ASN A 155 " pdb=" H ASN A 155 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N ASN C 155 " pdb=" H ASN C 155 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N ALA C 222 " pdb=" H ALA C 222 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.37: 25122 7.37 - 14.73: 24 14.73 - 22.10: 3 22.10 - 29.46: 0 29.46 - 36.83: 18 Bond angle restraints: 25167 Sorted by residual: angle pdb=" C MET C 101 " pdb=" CA MET C 101 " pdb=" HA MET C 101 " ideal model delta sigma weight residual 110.00 73.17 36.83 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C MET B 101 " pdb=" CA MET B 101 " pdb=" HA MET B 101 " ideal model delta sigma weight residual 110.00 73.20 36.80 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C MET A 101 " pdb=" CA MET A 101 " pdb=" HA MET A 101 " ideal model delta sigma weight residual 110.00 73.21 36.79 3.00e+00 1.11e-01 1.50e+02 angle pdb=" CB SER A 243 " pdb=" CA SER A 243 " pdb=" HA SER A 243 " ideal model delta sigma weight residual 109.00 73.80 35.20 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB SER B 243 " pdb=" CA SER B 243 " pdb=" HA SER B 243 " ideal model delta sigma weight residual 109.00 73.81 35.19 3.00e+00 1.11e-01 1.38e+02 ... (remaining 25162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 6384 28.54 - 57.09: 276 57.09 - 85.63: 51 85.63 - 114.17: 3 114.17 - 142.72: 12 Dihedral angle restraints: 6726 sinusoidal: 3675 harmonic: 3051 Sorted by residual: dihedral pdb=" C1 CLR A 401 " pdb=" C2 CLR A 401 " pdb=" C3 CLR A 401 " pdb=" O1 CLR A 401 " ideal model delta sinusoidal sigma weight residual 180.04 37.32 142.72 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C1 CLR C 401 " pdb=" C2 CLR C 401 " pdb=" C3 CLR C 401 " pdb=" O1 CLR C 401 " ideal model delta sinusoidal sigma weight residual 180.04 37.34 142.70 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C1 CLR B 401 " pdb=" C2 CLR B 401 " pdb=" C3 CLR B 401 " pdb=" O1 CLR B 401 " ideal model delta sinusoidal sigma weight residual 180.04 37.36 142.68 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 6723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 963 0.100 - 0.199: 78 0.199 - 0.299: 0 0.299 - 0.398: 9 0.398 - 0.498: 6 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C17 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C16 CLR A 401 " pdb=" C20 CLR A 401 " both_signs ideal model delta sigma weight residual False 2.55 3.05 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" C17 CLR C 401 " pdb=" C13 CLR C 401 " pdb=" C16 CLR C 401 " pdb=" C20 CLR C 401 " both_signs ideal model delta sigma weight residual False 2.55 3.05 -0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" C17 CLR B 401 " pdb=" C13 CLR B 401 " pdb=" C16 CLR B 401 " pdb=" C20 CLR B 401 " both_signs ideal model delta sigma weight residual False 2.55 3.05 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 1053 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 221 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C GLN C 221 " 0.051 2.00e-02 2.50e+03 pdb=" O GLN C 221 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 222 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 221 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C GLN B 221 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN B 221 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 222 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 221 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C GLN A 221 " 0.051 2.00e-02 2.50e+03 pdb=" O GLN A 221 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 222 " -0.017 2.00e-02 2.50e+03 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1057 2.21 - 2.81: 28283 2.81 - 3.41: 36368 3.41 - 4.00: 48496 4.00 - 4.60: 73742 Nonbonded interactions: 187946 Sorted by model distance: nonbonded pdb=" H SER C 243 " pdb=" HA SER C 243 " model vdw 1.613 1.816 nonbonded pdb=" H SER B 243 " pdb=" HA SER B 243 " model vdw 1.613 1.816 nonbonded pdb=" H SER A 243 " pdb=" HA SER A 243 " model vdw 1.613 1.816 nonbonded pdb=" H MET C 101 " pdb=" HA MET C 101 " model vdw 1.625 1.816 nonbonded pdb=" H MET A 101 " pdb=" HA MET A 101 " model vdw 1.625 1.816 ... (remaining 187941 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.240 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.007 0.106 7062 Z= 0.410 Angle : 1.010 16.997 9570 Z= 0.518 Chirality : 0.066 0.498 1056 Planarity : 0.006 0.048 1185 Dihedral : 18.384 142.715 2769 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.81 % Allowed : 0.40 % Favored : 98.79 % 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 aren not related in a simple way. whole: 1.27 (0.29), residues: 828 helix: 2.99 (0.30), residues: 279 sheet: 0.29 (0.27), residues: 327 loop : -1.09 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 153 TYR 0.027 0.002 TYR A 156 PHE 0.014 0.001 PHE B 204 TRP 0.004 0.001 TRP B 304 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 7059) covalent geometry : angle 1.00957 ( 9564) SS BOND : bond 0.02953 ( 3) SS BOND : angle 1.55024 ( 6) hydrogen bonds : bond 0.09650 ( 388) hydrogen bonds : angle 5.44781 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.368 Fit side-chains REVERT: B 148 ASN cc_start: 0.7244 (t0) cc_final: 0.6983 (t0) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 0.9675 time to fit residues: 93.5783 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.184376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144160 restraints weight = 21257.079| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.00 r_work: 0.3431 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7062 Z= 0.143 Angle : 0.593 7.068 9570 Z= 0.301 Chirality : 0.052 0.392 1056 Planarity : 0.005 0.042 1185 Dihedral : 10.796 88.820 1106 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.48 % Allowed : 6.45 % Favored : 92.07 % 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 aren not related in a simple way. whole: 1.24 (0.30), residues: 828 helix: 3.01 (0.30), residues: 282 sheet: 0.18 (0.27), residues: 327 loop : -1.08 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.011 0.001 TYR A 201 PHE 0.016 0.001 PHE B 204 TRP 0.006 0.001 TRP C 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7059) covalent geometry : angle 0.59337 ( 9564) SS BOND : bond 0.00209 ( 3) SS BOND : angle 0.56378 ( 6) hydrogen bonds : bond 0.04000 ( 388) hydrogen bonds : angle 4.82861 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.254 Fit side-chains REVERT: B 148 ASN cc_start: 0.7167 (t0) cc_final: 0.6718 (t0) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.7484 time to fit residues: 67.7919 Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.181796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138651 restraints weight = 21377.092| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.14 r_work: 0.3381 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7062 Z= 0.182 Angle : 0.573 6.081 9570 Z= 0.299 Chirality : 0.052 0.390 1056 Planarity : 0.005 0.035 1185 Dihedral : 7.056 58.015 1104 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.15 % Allowed : 7.26 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.30), residues: 828 helix: 3.05 (0.29), residues: 282 sheet: 0.08 (0.27), residues: 327 loop : -1.27 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.012 0.002 TYR A 201 PHE 0.019 0.001 PHE B 204 TRP 0.007 0.001 TRP A 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7059) covalent geometry : angle 0.57306 ( 9564) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.23860 ( 6) hydrogen bonds : bond 0.03944 ( 388) hydrogen bonds : angle 4.69210 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.414 Fit side-chains REVERT: B 161 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7525 (t) outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 0.8516 time to fit residues: 71.8338 Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139146 restraints weight = 21410.176| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.12 r_work: 0.3383 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7062 Z= 0.149 Angle : 0.540 6.335 9570 Z= 0.284 Chirality : 0.051 0.386 1056 Planarity : 0.004 0.035 1185 Dihedral : 6.391 57.923 1104 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.88 % Allowed : 7.93 % Favored : 90.19 % 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 aren not related in a simple way. whole: 1.19 (0.30), residues: 828 helix: 3.17 (0.29), residues: 282 sheet: 0.04 (0.27), residues: 327 loop : -1.22 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.010 0.001 TYR A 201 PHE 0.016 0.001 PHE A 204 TRP 0.007 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7059) covalent geometry : angle 0.54015 ( 9564) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.25248 ( 6) hydrogen bonds : bond 0.03775 ( 388) hydrogen bonds : angle 4.60829 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.407 Fit side-chains REVERT: A 147 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6579 (mtt) REVERT: B 161 SER cc_start: 0.7957 (m) cc_final: 0.7524 (t) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.8192 time to fit residues: 68.3777 Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 172 GLN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139018 restraints weight = 21592.425| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.12 r_work: 0.3373 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7062 Z= 0.146 Angle : 0.538 6.038 9570 Z= 0.283 Chirality : 0.051 0.389 1056 Planarity : 0.004 0.052 1185 Dihedral : 5.991 54.682 1103 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.02 % Allowed : 8.74 % Favored : 89.25 % 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 aren not related in a simple way. whole: 1.22 (0.30), residues: 828 helix: 3.29 (0.29), residues: 282 sheet: 0.03 (0.27), residues: 327 loop : -1.28 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 153 TYR 0.009 0.001 TYR A 201 PHE 0.017 0.001 PHE A 204 TRP 0.008 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7059) covalent geometry : angle 0.53821 ( 9564) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.23448 ( 6) hydrogen bonds : bond 0.03710 ( 388) hydrogen bonds : angle 4.55624 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.387 Fit side-chains REVERT: A 147 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6516 (mtt) REVERT: B 161 SER cc_start: 0.7969 (m) cc_final: 0.7553 (t) REVERT: C 129 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (mmtm) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.6528 time to fit residues: 51.5885 Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140429 restraints weight = 21323.609| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.10 r_work: 0.3387 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7062 Z= 0.120 Angle : 0.517 6.018 9570 Z= 0.272 Chirality : 0.050 0.387 1056 Planarity : 0.004 0.033 1185 Dihedral : 5.716 54.460 1103 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.28 % Allowed : 9.54 % Favored : 88.17 % 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 aren not related in a simple way. whole: 1.26 (0.30), residues: 828 helix: 3.38 (0.28), residues: 282 sheet: 0.09 (0.28), residues: 309 loop : -1.32 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 153 TYR 0.008 0.001 TYR A 201 PHE 0.015 0.001 PHE A 204 TRP 0.007 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7059) covalent geometry : angle 0.51713 ( 9564) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.21218 ( 6) hydrogen bonds : bond 0.03607 ( 388) hydrogen bonds : angle 4.45039 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.402 Fit side-chains REVERT: B 161 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7726 (t) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 0.7172 time to fit residues: 55.2317 Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.182481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141616 restraints weight = 21316.944| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.00 r_work: 0.3384 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7062 Z= 0.133 Angle : 0.521 6.002 9570 Z= 0.273 Chirality : 0.051 0.388 1056 Planarity : 0.004 0.033 1185 Dihedral : 5.537 54.464 1103 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.61 % Allowed : 10.48 % Favored : 87.90 % 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 aren not related in a simple way. whole: 1.28 (0.30), residues: 828 helix: 3.39 (0.28), residues: 282 sheet: 0.01 (0.27), residues: 327 loop : -1.26 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 TYR 0.010 0.001 TYR A 201 PHE 0.016 0.001 PHE A 204 TRP 0.007 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7059) covalent geometry : angle 0.52080 ( 9564) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.18670 ( 6) hydrogen bonds : bond 0.03566 ( 388) hydrogen bonds : angle 4.41982 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.369 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.7999 time to fit residues: 63.8643 Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.182518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141663 restraints weight = 21369.541| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.01 r_work: 0.3390 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7062 Z= 0.131 Angle : 0.520 5.894 9570 Z= 0.273 Chirality : 0.050 0.386 1056 Planarity : 0.004 0.033 1185 Dihedral : 5.408 54.207 1103 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.75 % Allowed : 10.89 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.30), residues: 828 helix: 3.41 (0.28), residues: 282 sheet: 0.08 (0.28), residues: 309 loop : -1.33 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.009 0.001 TYR A 201 PHE 0.015 0.001 PHE A 204 TRP 0.007 0.001 TRP C 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7059) covalent geometry : angle 0.52022 ( 9564) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.18638 ( 6) hydrogen bonds : bond 0.03537 ( 388) hydrogen bonds : angle 4.38916 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.397 Fit side-chains REVERT: A 307 ILE cc_start: 0.8331 (mm) cc_final: 0.8095 (mp) REVERT: B 161 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7757 (t) outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 0.7710 time to fit residues: 59.8866 Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.182253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139565 restraints weight = 21456.116| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.12 r_work: 0.3380 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7062 Z= 0.136 Angle : 0.521 6.053 9570 Z= 0.274 Chirality : 0.050 0.386 1056 Planarity : 0.004 0.033 1185 Dihedral : 5.311 54.011 1103 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.75 % Allowed : 11.29 % Favored : 86.96 % 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 aren not related in a simple way. whole: 1.25 (0.30), residues: 828 helix: 3.41 (0.28), residues: 282 sheet: 0.07 (0.28), residues: 309 loop : -1.36 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.009 0.001 TYR A 201 PHE 0.016 0.001 PHE A 204 TRP 0.008 0.001 TRP C 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7059) covalent geometry : angle 0.52083 ( 9564) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.20049 ( 6) hydrogen bonds : bond 0.03517 ( 388) hydrogen bonds : angle 4.38298 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.382 Fit side-chains REVERT: A 307 ILE cc_start: 0.8318 (mm) cc_final: 0.8082 (mp) outliers start: 13 outliers final: 12 residues processed: 70 average time/residue: 0.7627 time to fit residues: 58.4411 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 34 optimal weight: 0.0270 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.183751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143332 restraints weight = 21288.411| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.00 r_work: 0.3406 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7062 Z= 0.106 Angle : 0.508 5.984 9570 Z= 0.266 Chirality : 0.050 0.383 1056 Planarity : 0.004 0.032 1185 Dihedral : 5.140 53.965 1103 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.48 % Allowed : 11.56 % Favored : 86.96 % 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 aren not related in a simple way. whole: 1.32 (0.30), residues: 828 helix: 3.47 (0.28), residues: 282 sheet: 0.10 (0.28), residues: 309 loop : -1.31 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.006 0.001 TYR A 201 PHE 0.014 0.001 PHE A 204 TRP 0.008 0.001 TRP C 304 HIS 0.001 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7059) covalent geometry : angle 0.50860 ( 9564) SS BOND : bond 0.00015 ( 3) SS BOND : angle 0.14303 ( 6) hydrogen bonds : bond 0.03439 ( 388) hydrogen bonds : angle 4.29631 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.427 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 69 average time/residue: 0.7925 time to fit residues: 59.7622 Evaluate side-chains 73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.182831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141991 restraints weight = 21446.647| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.01 r_work: 0.3400 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7062 Z= 0.130 Angle : 0.518 5.937 9570 Z= 0.272 Chirality : 0.050 0.385 1056 Planarity : 0.004 0.033 1185 Dihedral : 5.129 53.565 1103 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.34 % Allowed : 11.69 % Favored : 86.96 % 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 aren not related in a simple way. whole: 1.30 (0.30), residues: 828 helix: 3.44 (0.28), residues: 282 sheet: 0.13 (0.28), residues: 309 loop : -1.36 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.009 0.001 TYR A 201 PHE 0.016 0.001 PHE A 204 TRP 0.007 0.001 TRP C 304 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7059) covalent geometry : angle 0.51858 ( 9564) SS BOND : bond 0.00058 ( 3) SS BOND : angle 0.16792 ( 6) hydrogen bonds : bond 0.03448 ( 388) hydrogen bonds : angle 4.29782 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.11 seconds wall clock time: 80 minutes 33.71 seconds (4833.71 seconds total)