Starting phenix.real_space_refine on Wed Sep 17 22:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdz_60018/09_2025/8zdz_60018.map" } resolution = 2.64 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= 0.005 sd= 0.029 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 80 5.16 5 C 7844 2.51 5 N 2012 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12024 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3006 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 6, 'TRANS': 367} Chain breaks: 2 Restraints were copied for chains: D, C, B Time building chain proxies: 2.69, per 1000 atoms: 0.22 Number of scatterers: 12024 At special positions: 0 Unit cell: (109.044, 109.044, 96.928, 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 80 16.00 O 2088 8.00 N 2012 7.00 C 7844 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: 1.16 Conformation dependent library (CDL) restraints added in 534.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 84.8% alpha, 2.9% 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 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.547A pdb=" N PHE A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.760A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 216 Proline residue: A 177 - end of helix removed outlier: 3.804A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 321 removed outlier: 6.012A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 357 removed outlier: 3.844A pdb=" N VAL A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.505A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.635A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.784A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.547A pdb=" N PHE D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.760A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 216 Proline residue: D 177 - end of helix removed outlier: 3.805A pdb=" N TYR D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 321 removed outlier: 6.011A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 357 removed outlier: 3.844A pdb=" N VAL D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 367 removed outlier: 3.506A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.634A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 421 removed outlier: 3.784A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.546A pdb=" N PHE C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 removed outlier: 3.759A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 216 Proline residue: C 177 - end of helix removed outlier: 3.804A pdb=" N TYR C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 321 removed outlier: 6.012A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 357 removed outlier: 3.844A pdb=" N VAL C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 367 removed outlier: 3.507A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.634A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 421 removed outlier: 3.785A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.547A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 removed outlier: 3.759A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 216 Proline residue: B 177 - end of helix removed outlier: 3.804A pdb=" N TYR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 321 removed outlier: 6.011A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 357 removed outlier: 3.844A pdb=" N VAL B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.507A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.634A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.784A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 5.406A pdb=" N GLN A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.406A pdb=" N GLN D 31 " --> pdb=" O ASN D 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.407A pdb=" N GLN C 31 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.406A pdb=" N GLN B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 3096 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: 2.07 Time building geometry restraints manager: 1.52 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: 3719 1.34 - 1.46: 2524 1.46 - 1.58: 5885 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 12256 Sorted by residual: bond pdb=" CB PRO C 372 " pdb=" CG PRO C 372 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.56e+00 bond pdb=" CB PRO A 372 " pdb=" CG PRO A 372 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.55e+00 bond pdb=" CB PRO D 372 " pdb=" CG PRO D 372 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.55e+00 bond pdb=" CB PRO B 372 " pdb=" CG PRO B 372 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.54e+00 bond pdb=" CB GLU D 376 " pdb=" CG GLU D 376 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 12251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 16222 1.72 - 3.44: 252 3.44 - 5.16: 86 5.16 - 6.88: 24 6.88 - 8.60: 4 Bond angle restraints: 16588 Sorted by residual: angle pdb=" CA GLU B 376 " pdb=" CB GLU B 376 " pdb=" CG GLU B 376 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.31e+00 angle pdb=" CA GLU A 376 " pdb=" CB GLU A 376 " pdb=" CG GLU A 376 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.22e+00 angle pdb=" CA GLU C 376 " pdb=" CB GLU C 376 " pdb=" CG GLU C 376 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.20e+00 angle pdb=" CA GLU D 376 " pdb=" CB GLU D 376 " pdb=" CG GLU D 376 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" CD PRO D 372 " ideal model delta sigma weight residual 112.00 108.50 3.50 1.40e+00 5.10e-01 6.24e+00 ... (remaining 16583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 5848 15.04 - 30.07: 940 30.07 - 45.11: 404 45.11 - 60.15: 100 60.15 - 75.18: 12 Dihedral angle restraints: 7304 sinusoidal: 2888 harmonic: 4416 Sorted by residual: dihedral pdb=" CA GLN B 31 " pdb=" C GLN B 31 " pdb=" N LEU B 32 " pdb=" CA LEU B 32 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN A 31 " pdb=" C GLN A 31 " pdb=" N LEU A 32 " pdb=" CA LEU A 32 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N LEU D 32 " pdb=" CA LEU D 32 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1439 0.039 - 0.078: 430 0.078 - 0.117: 78 0.117 - 0.156: 9 0.156 - 0.194: 12 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" C PRO D 372 " pdb=" CB PRO D 372 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA PRO B 372 " pdb=" N PRO B 372 " pdb=" C PRO B 372 " pdb=" CB PRO B 372 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA PRO C 372 " pdb=" N PRO C 372 " pdb=" C PRO C 372 " pdb=" CB PRO C 372 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1965 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 371 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO D 372 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 371 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO A 372 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 371 " -0.052 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 372 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " -0.043 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2835 2.79 - 3.32: 12387 3.32 - 3.84: 21048 3.84 - 4.37: 22387 4.37 - 4.90: 39767 Nonbonded interactions: 98424 Sorted by model distance: nonbonded pdb=" OE1 GLU D 279 " pdb=" NH1 ARG C 367 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG D 367 " pdb=" OE1 GLU B 279 " model vdw 2.289 3.120 nonbonded pdb=" OD1 ASN A 123 " pdb=" N ASN A 124 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASN C 123 " pdb=" N ASN C 124 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASN D 123 " pdb=" N ASN D 124 " model vdw 2.311 3.120 ... (remaining 98419 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.260 Find NCS groups from input model: 0.090 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.004 0.062 12256 Z= 0.154 Angle : 0.630 8.602 16588 Z= 0.318 Chirality : 0.039 0.194 1968 Planarity : 0.005 0.078 2008 Dihedral : 17.960 75.182 4440 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.35 % Allowed : 36.74 % Favored : 60.91 % 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: 2.47 (0.22), residues: 1472 helix: 2.44 (0.14), residues: 1216 sheet: -1.84 (0.63), residues: 48 loop : -2.68 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 272 TYR 0.012 0.001 TYR D 214 PHE 0.019 0.001 PHE A 61 TRP 0.010 0.001 TRP A 174 HIS 0.002 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00354 (12256) covalent geometry : angle 0.63007 (16588) hydrogen bonds : bond 0.08944 ( 1032) hydrogen bonds : angle 4.82328 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8981 (t70) cc_final: 0.8722 (t0) REVERT: A 159 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8255 (pp30) REVERT: A 318 MET cc_start: 0.6871 (tmm) cc_final: 0.6598 (tmm) REVERT: D 159 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8144 (pp30) REVERT: C 159 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8194 (pp30) REVERT: B 62 ASP cc_start: 0.9003 (t0) cc_final: 0.8768 (t0) REVERT: B 159 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8140 (pp30) outliers start: 31 outliers final: 15 residues processed: 264 average time/residue: 0.4032 time to fit residues: 120.0291 Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 302 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN C 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.104685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071849 restraints weight = 19414.279| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.88 r_work: 0.2713 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12256 Z= 0.162 Angle : 0.564 9.168 16588 Z= 0.284 Chirality : 0.038 0.147 1968 Planarity : 0.003 0.041 2008 Dihedral : 4.460 47.650 1655 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.23 % Allowed : 31.74 % Favored : 63.03 % 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: 3.36 (0.22), residues: 1472 helix: 3.00 (0.14), residues: 1228 sheet: -1.68 (0.63), residues: 48 loop : -2.27 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.011 0.001 TYR B 214 PHE 0.015 0.001 PHE A 370 TRP 0.006 0.001 TRP C 174 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00377 (12256) covalent geometry : angle 0.56423 (16588) hydrogen bonds : bond 0.04393 ( 1032) hydrogen bonds : angle 3.80792 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.488 Fit side-chains REVERT: A 51 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7885 (mpt) REVERT: A 123 ASN cc_start: 0.7532 (m-40) cc_final: 0.7153 (p0) REVERT: A 159 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8348 (pp30) REVERT: A 318 MET cc_start: 0.6843 (tmm) cc_final: 0.6624 (tmm) REVERT: A 376 GLU cc_start: 0.8885 (tp30) cc_final: 0.8608 (tp30) REVERT: D 51 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7876 (mpt) REVERT: D 99 MET cc_start: 0.9226 (tpt) cc_final: 0.9007 (tpt) REVERT: D 159 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8165 (pp30) REVERT: D 376 GLU cc_start: 0.8870 (tp30) cc_final: 0.8534 (tm-30) REVERT: C 31 GLN cc_start: 0.6591 (mm-40) cc_final: 0.6029 (tp40) REVERT: C 51 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7848 (mpt) REVERT: C 123 ASN cc_start: 0.7571 (m-40) cc_final: 0.7165 (p0) REVERT: C 159 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8269 (pp30) REVERT: C 279 GLU cc_start: 0.8666 (tt0) cc_final: 0.8379 (tt0) REVERT: C 376 GLU cc_start: 0.8874 (tp30) cc_final: 0.8622 (tp30) REVERT: B 31 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6174 (tp40) REVERT: B 51 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7857 (mpt) REVERT: B 123 ASN cc_start: 0.7595 (m-40) cc_final: 0.7197 (p0) REVERT: B 159 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8341 (pp30) REVERT: B 376 GLU cc_start: 0.8886 (tp30) cc_final: 0.8614 (tp30) outliers start: 69 outliers final: 19 residues processed: 236 average time/residue: 0.4297 time to fit residues: 113.6512 Evaluate side-chains 207 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 80 optimal weight: 5.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071711 restraints weight = 19554.543| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.92 r_work: 0.2733 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12256 Z= 0.133 Angle : 0.548 8.553 16588 Z= 0.274 Chirality : 0.037 0.141 1968 Planarity : 0.003 0.027 2008 Dihedral : 4.406 55.256 1644 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.15 % Allowed : 30.76 % Favored : 64.09 % 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: 3.58 (0.21), residues: 1472 helix: 3.17 (0.14), residues: 1228 sheet: -1.40 (0.65), residues: 48 loop : -2.42 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.012 0.001 TYR B 214 PHE 0.008 0.001 PHE D 291 TRP 0.007 0.001 TRP C 154 HIS 0.002 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00295 (12256) covalent geometry : angle 0.54844 (16588) hydrogen bonds : bond 0.04183 ( 1032) hydrogen bonds : angle 3.67234 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 0.507 Fit side-chains REVERT: A 85 SER cc_start: 0.8897 (p) cc_final: 0.8652 (m) REVERT: A 123 ASN cc_start: 0.7598 (m-40) cc_final: 0.7202 (p0) REVERT: A 159 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8362 (pp30) REVERT: A 323 ASP cc_start: 0.5929 (t70) cc_final: 0.5569 (p0) REVERT: A 376 GLU cc_start: 0.8903 (tp30) cc_final: 0.8513 (tp30) REVERT: D 51 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7874 (mpt) REVERT: D 85 SER cc_start: 0.8899 (p) cc_final: 0.8632 (m) REVERT: D 376 GLU cc_start: 0.8898 (tp30) cc_final: 0.8548 (tm-30) REVERT: C 85 SER cc_start: 0.8877 (p) cc_final: 0.8620 (m) REVERT: C 123 ASN cc_start: 0.7623 (m-40) cc_final: 0.7250 (p0) REVERT: C 279 GLU cc_start: 0.8669 (tt0) cc_final: 0.8359 (tt0) REVERT: C 376 GLU cc_start: 0.8907 (tp30) cc_final: 0.8629 (tp30) REVERT: B 85 SER cc_start: 0.8892 (p) cc_final: 0.8630 (m) REVERT: B 376 GLU cc_start: 0.8924 (tp30) cc_final: 0.8528 (tm-30) outliers start: 68 outliers final: 20 residues processed: 227 average time/residue: 0.4160 time to fit residues: 106.0470 Evaluate side-chains 202 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 388 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 421 GLN D 421 GLN C 171 ASN C 421 GLN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.067862 restraints weight = 19477.529| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.88 r_work: 0.2655 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12256 Z= 0.216 Angle : 0.608 8.362 16588 Z= 0.302 Chirality : 0.039 0.145 1968 Planarity : 0.003 0.024 2008 Dihedral : 4.261 50.474 1644 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.83 % Allowed : 29.77 % Favored : 64.39 % 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: 3.53 (0.21), residues: 1472 helix: 3.13 (0.14), residues: 1228 sheet: -1.20 (0.67), residues: 48 loop : -2.43 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.013 0.001 TYR A 214 PHE 0.011 0.001 PHE A 370 TRP 0.009 0.001 TRP A 154 HIS 0.005 0.002 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00512 (12256) covalent geometry : angle 0.60768 (16588) hydrogen bonds : bond 0.04821 ( 1032) hydrogen bonds : angle 3.78462 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.560 Fit side-chains REVERT: A 159 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8368 (pp30) REVERT: A 376 GLU cc_start: 0.8977 (tp30) cc_final: 0.8682 (tp30) REVERT: A 379 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8877 (tppp) REVERT: D 51 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7882 (mpt) REVERT: D 376 GLU cc_start: 0.8968 (tp30) cc_final: 0.8554 (tm-30) REVERT: C 279 GLU cc_start: 0.8767 (tt0) cc_final: 0.8460 (tt0) REVERT: C 376 GLU cc_start: 0.8984 (tp30) cc_final: 0.8664 (tp30) REVERT: C 379 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8886 (tppp) REVERT: B 376 GLU cc_start: 0.9006 (tp30) cc_final: 0.8533 (tm-30) outliers start: 77 outliers final: 23 residues processed: 232 average time/residue: 0.4263 time to fit residues: 110.6318 Evaluate side-chains 178 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 423 GLN D 421 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.068720 restraints weight = 19634.787| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.86 r_work: 0.2680 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12256 Z= 0.182 Angle : 0.598 8.519 16588 Z= 0.295 Chirality : 0.038 0.147 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.902 36.775 1644 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.94 % Allowed : 31.89 % Favored : 64.17 % 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: 3.62 (0.22), residues: 1472 helix: 3.18 (0.14), residues: 1228 sheet: -1.07 (0.68), residues: 48 loop : -2.39 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.015 0.001 TYR D 292 PHE 0.008 0.001 PHE B 291 TRP 0.009 0.001 TRP D 154 HIS 0.004 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00425 (12256) covalent geometry : angle 0.59762 (16588) hydrogen bonds : bond 0.04567 ( 1032) hydrogen bonds : angle 3.70384 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.611 Fit side-chains REVERT: A 290 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8130 (ttp80) REVERT: A 376 GLU cc_start: 0.8998 (tp30) cc_final: 0.8491 (tm-30) REVERT: A 421 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8278 (pp30) REVERT: D 51 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7965 (mpt) REVERT: D 290 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8124 (ttp80) REVERT: D 376 GLU cc_start: 0.8993 (tp30) cc_final: 0.8552 (tm-30) REVERT: C 279 GLU cc_start: 0.8761 (tt0) cc_final: 0.8479 (tt0) REVERT: C 290 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: C 376 GLU cc_start: 0.8991 (tp30) cc_final: 0.8642 (tp30) REVERT: C 379 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8888 (tppp) REVERT: B 290 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8141 (ttp80) REVERT: B 376 GLU cc_start: 0.9014 (tp30) cc_final: 0.8508 (tm-30) outliers start: 52 outliers final: 23 residues processed: 197 average time/residue: 0.5078 time to fit residues: 110.2150 Evaluate side-chains 182 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 421 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 277 ASN D 421 GLN C 330 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.072756 restraints weight = 19404.109| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.85 r_work: 0.2728 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12256 Z= 0.121 Angle : 0.570 9.078 16588 Z= 0.284 Chirality : 0.037 0.151 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.718 26.881 1644 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.26 % Allowed : 32.35 % Favored : 64.39 % 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: 3.84 (0.22), residues: 1472 helix: 3.31 (0.14), residues: 1232 sheet: -1.09 (0.67), residues: 48 loop : -2.25 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 272 TYR 0.011 0.001 TYR A 292 PHE 0.027 0.001 PHE A 422 TRP 0.010 0.001 TRP D 154 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00253 (12256) covalent geometry : angle 0.56989 (16588) hydrogen bonds : bond 0.04041 ( 1032) hydrogen bonds : angle 3.57505 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.486 Fit side-chains REVERT: A 376 GLU cc_start: 0.8977 (tp30) cc_final: 0.8490 (tm-30) REVERT: D 51 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7940 (mpt) REVERT: D 376 GLU cc_start: 0.9004 (tp30) cc_final: 0.8571 (tm-30) REVERT: C 279 GLU cc_start: 0.8704 (tt0) cc_final: 0.8443 (tt0) REVERT: C 376 GLU cc_start: 0.8980 (tp30) cc_final: 0.8527 (tm-30) REVERT: B 376 GLU cc_start: 0.9000 (tp30) cc_final: 0.8516 (tm-30) outliers start: 43 outliers final: 24 residues processed: 189 average time/residue: 0.4567 time to fit residues: 96.1509 Evaluate side-chains 181 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 421 GLN C 421 GLN B 171 ASN B 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.067960 restraints weight = 19555.643| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.84 r_work: 0.2653 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12256 Z= 0.237 Angle : 0.639 9.970 16588 Z= 0.320 Chirality : 0.040 0.147 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.769 29.298 1644 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.94 % Allowed : 30.91 % Favored : 65.15 % 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: 3.72 (0.22), residues: 1472 helix: 3.21 (0.14), residues: 1232 sheet: -1.04 (0.69), residues: 48 loop : -2.18 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 340 TYR 0.013 0.001 TYR A 292 PHE 0.031 0.001 PHE C 422 TRP 0.008 0.001 TRP D 154 HIS 0.007 0.002 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00560 (12256) covalent geometry : angle 0.63917 (16588) hydrogen bonds : bond 0.04796 ( 1032) hydrogen bonds : angle 3.74624 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.511 Fit side-chains REVERT: A 376 GLU cc_start: 0.9017 (tp30) cc_final: 0.8661 (tp30) REVERT: D 51 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7979 (mpt) REVERT: D 376 GLU cc_start: 0.9026 (tp30) cc_final: 0.8545 (tm-30) REVERT: C 83 ASP cc_start: 0.8207 (t0) cc_final: 0.7993 (t0) REVERT: C 279 GLU cc_start: 0.8793 (tt0) cc_final: 0.8533 (tt0) REVERT: C 290 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: C 376 GLU cc_start: 0.9014 (tp30) cc_final: 0.8643 (tp30) REVERT: C 422 PHE cc_start: 0.8051 (t80) cc_final: 0.7787 (t80) REVERT: B 83 ASP cc_start: 0.8197 (t0) cc_final: 0.7993 (t0) REVERT: B 290 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8127 (ttp80) REVERT: B 376 GLU cc_start: 0.9039 (tp30) cc_final: 0.8508 (tm-30) outliers start: 52 outliers final: 17 residues processed: 196 average time/residue: 0.5268 time to fit residues: 113.4698 Evaluate side-chains 168 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 290 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 421 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.069711 restraints weight = 19378.060| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.87 r_work: 0.2679 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12256 Z= 0.163 Angle : 0.633 10.327 16588 Z= 0.315 Chirality : 0.039 0.166 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.796 28.035 1644 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.73 % Allowed : 32.05 % Favored : 65.23 % 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: 3.74 (0.22), residues: 1472 helix: 3.24 (0.14), residues: 1232 sheet: -1.15 (0.68), residues: 48 loop : -2.19 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 340 TYR 0.011 0.001 TYR A 214 PHE 0.010 0.001 PHE B 422 TRP 0.008 0.001 TRP D 154 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00378 (12256) covalent geometry : angle 0.63274 (16588) hydrogen bonds : bond 0.04389 ( 1032) hydrogen bonds : angle 3.62084 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.518 Fit side-chains REVERT: A 376 GLU cc_start: 0.9008 (tp30) cc_final: 0.8498 (tm-30) REVERT: D 51 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7987 (mpt) REVERT: D 157 MET cc_start: 0.8239 (ttm) cc_final: 0.8033 (ptp) REVERT: D 376 GLU cc_start: 0.9036 (tp30) cc_final: 0.8565 (tm-30) REVERT: D 421 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8362 (pp30) REVERT: C 279 GLU cc_start: 0.8757 (tt0) cc_final: 0.8476 (tt0) REVERT: C 290 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: C 376 GLU cc_start: 0.9023 (tp30) cc_final: 0.8533 (tm-30) REVERT: B 16 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (mm) REVERT: B 376 GLU cc_start: 0.9016 (tp30) cc_final: 0.8500 (tm-30) outliers start: 36 outliers final: 17 residues processed: 172 average time/residue: 0.5360 time to fit residues: 101.1308 Evaluate side-chains 163 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 330 GLN D 421 GLN C 421 GLN B 330 GLN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072624 restraints weight = 19286.856| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.85 r_work: 0.2728 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12256 Z= 0.129 Angle : 0.629 10.789 16588 Z= 0.312 Chirality : 0.038 0.159 1968 Planarity : 0.003 0.023 2008 Dihedral : 3.795 26.780 1644 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.20 % Allowed : 32.58 % Favored : 65.23 % 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: 3.92 (0.22), residues: 1472 helix: 3.36 (0.14), residues: 1232 sheet: -1.21 (0.66), residues: 48 loop : -2.18 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 399 TYR 0.012 0.001 TYR C 179 PHE 0.015 0.001 PHE D 422 TRP 0.010 0.001 TRP D 154 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00279 (12256) covalent geometry : angle 0.62947 (16588) hydrogen bonds : bond 0.03951 ( 1032) hydrogen bonds : angle 3.52207 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.417 Fit side-chains REVERT: A 83 ASP cc_start: 0.7867 (t0) cc_final: 0.7562 (t0) REVERT: A 376 GLU cc_start: 0.8983 (tp30) cc_final: 0.8487 (tm-30) REVERT: D 51 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7937 (mpt) REVERT: D 83 ASP cc_start: 0.7869 (t0) cc_final: 0.7532 (t0) REVERT: D 376 GLU cc_start: 0.9021 (tp30) cc_final: 0.8548 (tm-30) REVERT: C 279 GLU cc_start: 0.8718 (tt0) cc_final: 0.8434 (tt0) REVERT: C 376 GLU cc_start: 0.8994 (tp30) cc_final: 0.8541 (tm-30) REVERT: B 376 GLU cc_start: 0.9008 (tp30) cc_final: 0.8502 (tm-30) outliers start: 29 outliers final: 15 residues processed: 177 average time/residue: 0.4534 time to fit residues: 89.6716 Evaluate side-chains 165 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 81 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 421 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.072801 restraints weight = 19389.126| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.88 r_work: 0.2732 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12256 Z= 0.132 Angle : 0.638 11.426 16588 Z= 0.314 Chirality : 0.038 0.157 1968 Planarity : 0.003 0.025 2008 Dihedral : 3.742 25.858 1644 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.44 % Allowed : 33.48 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.00 (0.22), residues: 1472 helix: 3.42 (0.13), residues: 1232 sheet: -1.35 (0.64), residues: 48 loop : -2.13 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 36 TYR 0.010 0.001 TYR A 214 PHE 0.035 0.001 PHE B 422 TRP 0.009 0.001 TRP D 154 HIS 0.004 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00292 (12256) covalent geometry : angle 0.63799 (16588) hydrogen bonds : bond 0.03865 ( 1032) hydrogen bonds : angle 3.50273 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.504 Fit side-chains REVERT: A 83 ASP cc_start: 0.7895 (t0) cc_final: 0.7674 (t0) REVERT: A 376 GLU cc_start: 0.8980 (tp30) cc_final: 0.8471 (tm-30) REVERT: D 51 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7937 (mpt) REVERT: D 83 ASP cc_start: 0.7887 (t0) cc_final: 0.7636 (t0) REVERT: D 157 MET cc_start: 0.8256 (ttm) cc_final: 0.8055 (ptp) REVERT: D 376 GLU cc_start: 0.9026 (tp30) cc_final: 0.8584 (tm-30) REVERT: C 83 ASP cc_start: 0.7887 (t0) cc_final: 0.7602 (t0) REVERT: C 279 GLU cc_start: 0.8692 (tt0) cc_final: 0.8430 (tt0) REVERT: C 376 GLU cc_start: 0.8982 (tp30) cc_final: 0.8511 (tm-30) REVERT: B 83 ASP cc_start: 0.7871 (t0) cc_final: 0.7588 (t0) REVERT: B 376 GLU cc_start: 0.9014 (tp30) cc_final: 0.8510 (tm-30) outliers start: 19 outliers final: 14 residues processed: 165 average time/residue: 0.4694 time to fit residues: 86.1747 Evaluate side-chains 161 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 421 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074144 restraints weight = 19309.381| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.87 r_work: 0.2746 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12256 Z= 0.128 Angle : 0.642 11.330 16588 Z= 0.314 Chirality : 0.037 0.155 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.516 19.521 1640 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.59 % Allowed : 33.11 % Favored : 65.30 % 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: 4.06 (0.22), residues: 1472 helix: 3.46 (0.13), residues: 1232 sheet: -1.32 (0.64), residues: 48 loop : -2.05 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 272 TYR 0.011 0.001 TYR C 179 PHE 0.008 0.001 PHE B 370 TRP 0.009 0.001 TRP D 154 HIS 0.004 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00278 (12256) covalent geometry : angle 0.64210 (16588) hydrogen bonds : bond 0.03742 ( 1032) hydrogen bonds : angle 3.46528 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3520.06 seconds wall clock time: 61 minutes 11.62 seconds (3671.62 seconds total)