Starting phenix.real_space_refine on Tue Jun 10 16:25:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdz_60018/06_2025/8zdz_60018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdz_60018/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zdz_60018/06_2025/8zdz_60018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdz_60018/06_2025/8zdz_60018.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdz_60018/06_2025/8zdz_60018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdz_60018/06_2025/8zdz_60018.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 6.43, per 1000 atoms: 0.53 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: 3.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 0.89 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: 3.55 Time building geometry restraints manager: 4.23 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.200 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.630 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.001 TRP A 174 HIS 0.002 0.001 HIS D 189 PHE 0.019 0.001 PHE A 61 TYR 0.012 0.001 TYR D 214 ARG 0.003 0.000 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.08944 ( 1032) hydrogen bonds : angle 4.82328 ( 3096) covalent geometry : bond 0.00354 (12256) covalent geometry : angle 0.63007 (16588) *********************** 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 : 1.448 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: 0.7751 time to fit residues: 231.1270 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 : 1.331 ------------------------------------------------------------------------------- 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 124 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.104650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071748 restraints weight = 19348.033| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.87 r_work: 0.2721 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12256 Z= 0.164 Angle : 0.566 9.166 16588 Z= 0.284 Chirality : 0.038 0.157 1968 Planarity : 0.003 0.041 2008 Dihedral : 4.466 47.220 1655 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.77 % Allowed : 32.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.22), residues: 1472 helix: 2.99 (0.14), residues: 1228 sheet: -1.67 (0.63), residues: 48 loop : -2.27 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 174 HIS 0.003 0.001 HIS A 189 PHE 0.015 0.001 PHE A 370 TYR 0.012 0.001 TYR B 214 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1032) hydrogen bonds : angle 3.81860 ( 3096) covalent geometry : bond 0.00382 (12256) covalent geometry : angle 0.56620 (16588) *********************** 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 257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 1.703 Fit side-chains REVERT: A 51 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7881 (mpt) REVERT: A 123 ASN cc_start: 0.7548 (m-40) cc_final: 0.7266 (p0) REVERT: A 159 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8358 (pp30) REVERT: A 318 MET cc_start: 0.6858 (tmm) cc_final: 0.6639 (tmm) REVERT: A 376 GLU cc_start: 0.8873 (tp30) cc_final: 0.8605 (tp30) REVERT: D 31 GLN cc_start: 0.6881 (mm-40) cc_final: 0.6226 (tp40) REVERT: D 51 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7875 (mpt) REVERT: D 99 MET cc_start: 0.9212 (tpt) cc_final: 0.9002 (tpt) REVERT: D 159 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8173 (pp30) REVERT: D 376 GLU cc_start: 0.8861 (tp30) cc_final: 0.8534 (tm-30) REVERT: C 31 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6002 (tp40) REVERT: C 51 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7849 (mpt) REVERT: C 123 ASN cc_start: 0.7611 (m-40) cc_final: 0.7233 (p0) REVERT: C 159 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8271 (pp30) REVERT: C 279 GLU cc_start: 0.8664 (tt0) cc_final: 0.8380 (tt0) REVERT: C 376 GLU cc_start: 0.8861 (tp30) cc_final: 0.8595 (tp30) REVERT: B 31 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6167 (tp40) REVERT: B 51 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7858 (mpt) REVERT: B 123 ASN cc_start: 0.7592 (m-40) cc_final: 0.7232 (p0) REVERT: B 159 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8335 (pp30) REVERT: B 376 GLU cc_start: 0.8880 (tp30) cc_final: 0.8622 (tp30) outliers start: 63 outliers final: 18 residues processed: 233 average time/residue: 0.9741 time to fit residues: 252.9844 Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 139 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: D 421 GLN C 421 GLN B 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.069579 restraints weight = 19478.815| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.88 r_work: 0.2685 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12256 Z= 0.182 Angle : 0.569 8.501 16588 Z= 0.288 Chirality : 0.038 0.145 1968 Planarity : 0.003 0.030 2008 Dihedral : 4.536 59.184 1644 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.29 % Allowed : 29.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.21), residues: 1472 helix: 3.11 (0.14), residues: 1228 sheet: -1.39 (0.66), residues: 48 loop : -2.45 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS C 189 PHE 0.009 0.001 PHE A 291 TYR 0.014 0.001 TYR A 214 ARG 0.003 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 1032) hydrogen bonds : angle 3.77115 ( 3096) covalent geometry : bond 0.00424 (12256) covalent geometry : angle 0.56937 (16588) *********************** 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 259 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 176 time to evaluate : 1.408 Fit side-chains REVERT: A 51 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7906 (mpt) REVERT: A 85 SER cc_start: 0.8879 (p) cc_final: 0.8660 (m) REVERT: A 159 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8372 (pp30) REVERT: A 318 MET cc_start: 0.6892 (tmm) cc_final: 0.6656 (tmm) REVERT: A 323 ASP cc_start: 0.6006 (t70) cc_final: 0.5552 (p0) REVERT: A 376 GLU cc_start: 0.8926 (tp30) cc_final: 0.8649 (tp30) REVERT: D 51 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7906 (mpt) REVERT: D 85 SER cc_start: 0.8878 (p) cc_final: 0.8639 (m) REVERT: D 376 GLU cc_start: 0.8930 (tp30) cc_final: 0.8573 (tm-30) REVERT: C 51 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7808 (mpt) REVERT: C 85 SER cc_start: 0.8886 (p) cc_final: 0.8655 (m) REVERT: C 99 MET cc_start: 0.9231 (tpt) cc_final: 0.9022 (tpt) REVERT: C 279 GLU cc_start: 0.8732 (tt0) cc_final: 0.8430 (tt0) REVERT: C 376 GLU cc_start: 0.8926 (tp30) cc_final: 0.8633 (tp30) REVERT: C 379 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8886 (tppp) REVERT: B 51 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7885 (mpt) REVERT: B 85 SER cc_start: 0.8871 (p) cc_final: 0.8636 (m) REVERT: B 376 GLU cc_start: 0.8933 (tp30) cc_final: 0.8652 (tp30) outliers start: 83 outliers final: 22 residues processed: 238 average time/residue: 0.8857 time to fit residues: 235.6442 Evaluate side-chains 206 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 69 VAL 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 151 VAL 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 374 LEU Chi-restraints excluded: chain C residue 51 MET 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 B residue 46 CYS Chi-restraints excluded: chain B residue 51 MET 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 271 ILE Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 421 GLN B 277 ASN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.071763 restraints weight = 19219.604| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.88 r_work: 0.2725 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12256 Z= 0.129 Angle : 0.563 8.450 16588 Z= 0.277 Chirality : 0.037 0.143 1968 Planarity : 0.003 0.025 2008 Dihedral : 4.245 50.373 1644 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.77 % Allowed : 30.76 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.21), residues: 1472 helix: 3.22 (0.14), residues: 1228 sheet: -1.28 (0.66), residues: 48 loop : -2.47 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 154 HIS 0.003 0.001 HIS D 306 PHE 0.010 0.001 PHE A 370 TYR 0.012 0.001 TYR B 214 ARG 0.002 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1032) hydrogen bonds : angle 3.62471 ( 3096) covalent geometry : bond 0.00283 (12256) covalent geometry : angle 0.56282 (16588) *********************** 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 232 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 1.500 Fit side-chains REVERT: A 123 ASN cc_start: 0.7512 (m-40) cc_final: 0.7045 (p0) REVERT: A 159 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8339 (pp30) REVERT: A 318 MET cc_start: 0.6889 (tmm) cc_final: 0.6679 (tmm) REVERT: A 376 GLU cc_start: 0.8948 (tp30) cc_final: 0.8649 (tp30) REVERT: D 51 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7880 (mpt) REVERT: D 376 GLU cc_start: 0.8925 (tp30) cc_final: 0.8511 (tm-30) REVERT: C 123 ASN cc_start: 0.7539 (m-40) cc_final: 0.7141 (p0) REVERT: C 279 GLU cc_start: 0.8704 (tt0) cc_final: 0.8399 (tt0) REVERT: C 376 GLU cc_start: 0.8953 (tp30) cc_final: 0.8655 (tp30) REVERT: B 51 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7888 (mpt) REVERT: B 123 ASN cc_start: 0.7439 (m-40) cc_final: 0.7015 (p0) REVERT: B 376 GLU cc_start: 0.8977 (tp30) cc_final: 0.8504 (tm-30) outliers start: 63 outliers final: 21 residues processed: 210 average time/residue: 0.9443 time to fit residues: 222.7374 Evaluate side-chains 189 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 69 VAL 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 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 374 LEU Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain C residue 16 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 B residue 46 CYS Chi-restraints excluded: chain B residue 51 MET 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 374 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 A 423 GLN D 421 GLN C 171 ASN C 421 GLN B 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.069025 restraints weight = 19280.196| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.86 r_work: 0.2685 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2354 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= 0.179 Angle : 0.591 8.541 16588 Z= 0.294 Chirality : 0.038 0.142 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.834 34.142 1644 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.77 % Allowed : 31.59 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.21), residues: 1472 helix: 3.23 (0.14), residues: 1228 sheet: -1.19 (0.67), residues: 48 loop : -2.45 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.006 0.001 HIS C 306 PHE 0.009 0.001 PHE C 291 TYR 0.012 0.001 TYR C 292 ARG 0.003 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 1032) hydrogen bonds : angle 3.70873 ( 3096) covalent geometry : bond 0.00417 (12256) covalent geometry : angle 0.59128 (16588) *********************** 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 223 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 1.573 Fit side-chains REVERT: A 318 MET cc_start: 0.6959 (tmm) cc_final: 0.6716 (tmm) REVERT: A 376 GLU cc_start: 0.8994 (tp30) cc_final: 0.8693 (tp30) REVERT: A 379 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8881 (tppp) REVERT: A 421 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (pp30) REVERT: D 51 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7933 (mpt) REVERT: D 376 GLU cc_start: 0.8984 (tp30) cc_final: 0.8549 (tm-30) REVERT: C 279 GLU cc_start: 0.8779 (tt0) cc_final: 0.8513 (tt0) REVERT: C 376 GLU cc_start: 0.8994 (tp30) cc_final: 0.8680 (tp30) REVERT: C 379 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8888 (tppp) REVERT: B 51 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7952 (mpt) REVERT: B 376 GLU cc_start: 0.9018 (tp30) cc_final: 0.8508 (tm-30) outliers start: 63 outliers final: 25 residues processed: 211 average time/residue: 1.0066 time to fit residues: 237.0823 Evaluate side-chains 177 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 69 VAL 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 208 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 421 GLN 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 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 16 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 B residue 46 CYS Chi-restraints excluded: chain B residue 51 MET 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 374 LEU 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 101 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 GLN C 330 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 = 0.3436 r_free = 0.3436 target = 0.102824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.070108 restraints weight = 19608.999| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.84 r_work: 0.2678 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2488 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= 0.175 Angle : 0.595 8.839 16588 Z= 0.297 Chirality : 0.038 0.146 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.748 29.112 1644 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.79 % Allowed : 31.36 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.22), residues: 1472 helix: 3.28 (0.14), residues: 1228 sheet: -1.18 (0.67), residues: 48 loop : -2.40 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.006 0.001 HIS B 306 PHE 0.026 0.001 PHE C 422 TYR 0.015 0.001 TYR D 292 ARG 0.003 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 1032) hydrogen bonds : angle 3.66455 ( 3096) covalent geometry : bond 0.00407 (12256) covalent geometry : angle 0.59502 (16588) *********************** 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 198 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.474 Fit side-chains REVERT: A 318 MET cc_start: 0.6962 (tmm) cc_final: 0.6715 (tmm) REVERT: A 376 GLU cc_start: 0.8997 (tp30) cc_final: 0.8685 (tp30) REVERT: D 51 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7974 (mpt) REVERT: D 376 GLU cc_start: 0.9005 (tp30) cc_final: 0.8556 (tm-30) REVERT: D 422 PHE cc_start: 0.8012 (t80) cc_final: 0.7808 (t80) REVERT: C 279 GLU cc_start: 0.8768 (tt0) cc_final: 0.8483 (tt0) REVERT: C 376 GLU cc_start: 0.8999 (tp30) cc_final: 0.8661 (tp30) REVERT: B 51 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7965 (mpt) REVERT: B 83 ASP cc_start: 0.8041 (t0) cc_final: 0.7827 (t0) REVERT: B 376 GLU cc_start: 0.9023 (tp30) cc_final: 0.8521 (tm-30) outliers start: 50 outliers final: 26 residues processed: 190 average time/residue: 1.1911 time to fit residues: 251.8049 Evaluate side-chains 182 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 117 SER 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 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 421 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 51 MET 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 151 VAL 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 40 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069481 restraints weight = 19327.692| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.86 r_work: 0.2686 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2616 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= 0.174 Angle : 0.604 9.773 16588 Z= 0.303 Chirality : 0.038 0.150 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.722 28.181 1644 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.64 % Allowed : 30.98 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.22), residues: 1472 helix: 3.28 (0.14), residues: 1232 sheet: -1.17 (0.67), residues: 48 loop : -2.25 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.006 0.001 HIS A 306 PHE 0.014 0.001 PHE C 422 TYR 0.014 0.001 TYR D 292 ARG 0.003 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 1032) hydrogen bonds : angle 3.65227 ( 3096) covalent geometry : bond 0.00408 (12256) covalent geometry : angle 0.60375 (16588) *********************** 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 199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.551 Fit side-chains REVERT: A 83 ASP cc_start: 0.8045 (t0) cc_final: 0.7835 (t0) REVERT: A 318 MET cc_start: 0.6946 (tmm) cc_final: 0.6700 (tmm) REVERT: A 376 GLU cc_start: 0.9016 (tp30) cc_final: 0.8690 (tp30) REVERT: D 51 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7997 (mpt) REVERT: D 83 ASP cc_start: 0.8038 (t0) cc_final: 0.7837 (t0) REVERT: D 376 GLU cc_start: 0.9012 (tp30) cc_final: 0.8534 (tm-30) REVERT: C 279 GLU cc_start: 0.8769 (tt0) cc_final: 0.8486 (tt0) REVERT: C 376 GLU cc_start: 0.9008 (tp30) cc_final: 0.8649 (tp30) REVERT: B 51 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7967 (mpt) REVERT: B 376 GLU cc_start: 0.9028 (tp30) cc_final: 0.8506 (tm-30) outliers start: 48 outliers final: 26 residues processed: 189 average time/residue: 1.1693 time to fit residues: 244.8235 Evaluate side-chains 174 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 208 GLN 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 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 343 MET 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 343 MET 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 51 MET 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 151 VAL Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 330 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 = 0.3436 r_free = 0.3436 target = 0.103346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.070313 restraints weight = 19490.515| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.88 r_work: 0.2698 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12256 Z= 0.156 Angle : 0.622 10.266 16588 Z= 0.312 Chirality : 0.038 0.156 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.757 27.686 1644 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.88 % Allowed : 31.44 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.22), residues: 1472 helix: 3.30 (0.13), residues: 1232 sheet: -1.25 (0.66), residues: 48 loop : -2.27 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS A 306 PHE 0.021 0.001 PHE D 422 TYR 0.013 0.001 TYR D 292 ARG 0.002 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 1032) hydrogen bonds : angle 3.58245 ( 3096) covalent geometry : bond 0.00360 (12256) covalent geometry : angle 0.62228 (16588) *********************** 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 188 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 2.529 Fit side-chains REVERT: A 318 MET cc_start: 0.6951 (tmm) cc_final: 0.6705 (tmm) REVERT: A 376 GLU cc_start: 0.9018 (tp30) cc_final: 0.8510 (tm-30) REVERT: D 51 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7990 (mpt) REVERT: D 376 GLU cc_start: 0.9019 (tp30) cc_final: 0.8549 (tm-30) REVERT: D 421 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: C 279 GLU cc_start: 0.8757 (tt0) cc_final: 0.8474 (tt0) REVERT: C 376 GLU cc_start: 0.9006 (tp30) cc_final: 0.8540 (tm-30) REVERT: C 421 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8260 (pp30) REVERT: B 51 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7964 (mpt) REVERT: B 376 GLU cc_start: 0.9022 (tp30) cc_final: 0.8519 (tm-30) outliers start: 38 outliers final: 27 residues processed: 180 average time/residue: 1.2269 time to fit residues: 246.8641 Evaluate side-chains 177 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 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 117 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 421 GLN 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 343 MET 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 51 MET 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 151 VAL 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 95 optimal weight: 0.0370 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.104537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071520 restraints weight = 19271.878| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.85 r_work: 0.2714 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2722 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= 0.137 Angle : 0.617 10.852 16588 Z= 0.309 Chirality : 0.037 0.158 1968 Planarity : 0.003 0.023 2008 Dihedral : 3.748 26.978 1644 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.50 % Allowed : 31.97 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.22), residues: 1472 helix: 3.33 (0.14), residues: 1232 sheet: -1.32 (0.66), residues: 48 loop : -2.22 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS B 306 PHE 0.012 0.001 PHE C 422 TYR 0.013 0.001 TYR B 179 ARG 0.002 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1032) hydrogen bonds : angle 3.53255 ( 3096) covalent geometry : bond 0.00304 (12256) covalent geometry : angle 0.61745 (16588) *********************** 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 182 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.355 Fit side-chains REVERT: A 318 MET cc_start: 0.6947 (tmm) cc_final: 0.6699 (tmm) REVERT: A 376 GLU cc_start: 0.9000 (tp30) cc_final: 0.8482 (tm-30) REVERT: D 51 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7946 (mpt) REVERT: D 376 GLU cc_start: 0.9023 (tp30) cc_final: 0.8541 (tm-30) REVERT: C 279 GLU cc_start: 0.8734 (tt0) cc_final: 0.8451 (tt0) REVERT: C 376 GLU cc_start: 0.9004 (tp30) cc_final: 0.8531 (tm-30) REVERT: B 51 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7951 (mpt) REVERT: B 376 GLU cc_start: 0.9010 (tp30) cc_final: 0.8504 (tm-30) outliers start: 33 outliers final: 22 residues processed: 174 average time/residue: 0.8594 time to fit residues: 167.9657 Evaluate side-chains 172 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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 343 MET 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 343 MET 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 51 MET 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 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 39 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 21 optimal weight: 0.0030 chunk 2 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.0370 overall best weight: 2.2074 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.102991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.070486 restraints weight = 19517.304| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.83 r_work: 0.2676 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2765 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= 0.180 Angle : 0.644 11.434 16588 Z= 0.323 Chirality : 0.039 0.183 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.772 28.076 1644 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.27 % Allowed : 32.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.22), residues: 1472 helix: 3.28 (0.14), residues: 1232 sheet: -1.32 (0.67), residues: 48 loop : -2.17 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.006 0.001 HIS A 306 PHE 0.010 0.001 PHE C 422 TYR 0.014 0.001 TYR C 179 ARG 0.003 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1032) hydrogen bonds : angle 3.61228 ( 3096) covalent geometry : bond 0.00420 (12256) covalent geometry : angle 0.64442 (16588) ********************** 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 176 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.496 Fit side-chains REVERT: A 318 MET cc_start: 0.6959 (tmm) cc_final: 0.6666 (tmm) REVERT: A 376 GLU cc_start: 0.9019 (tp30) cc_final: 0.8620 (tp30) REVERT: D 51 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7958 (mpt) REVERT: D 376 GLU cc_start: 0.9050 (tp30) cc_final: 0.8601 (tm-30) REVERT: C 279 GLU cc_start: 0.8718 (tt0) cc_final: 0.8501 (tt0) REVERT: C 376 GLU cc_start: 0.9016 (tp30) cc_final: 0.8593 (tp30) REVERT: B 51 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7962 (mpt) REVERT: B 376 GLU cc_start: 0.9018 (tp30) cc_final: 0.8617 (tp30) outliers start: 30 outliers final: 22 residues processed: 168 average time/residue: 0.9328 time to fit residues: 175.0321 Evaluate side-chains 164 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 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 D residue 421 GLN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 86 VAL 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 51 MET 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 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 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 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 = 0.3464 r_free = 0.3464 target = 0.105459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072576 restraints weight = 19188.047| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.84 r_work: 0.2731 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2790 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= 0.130 Angle : 0.627 11.361 16588 Z= 0.312 Chirality : 0.038 0.204 1968 Planarity : 0.003 0.023 2008 Dihedral : 3.763 26.411 1644 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.05 % Allowed : 32.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.22), residues: 1472 helix: 3.37 (0.14), residues: 1232 sheet: -1.41 (0.66), residues: 48 loop : -2.15 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 306 PHE 0.010 0.001 PHE D 370 TYR 0.014 0.001 TYR B 179 ARG 0.001 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1032) hydrogen bonds : angle 3.50216 ( 3096) covalent geometry : bond 0.00281 (12256) covalent geometry : angle 0.62667 (16588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7943.66 seconds wall clock time: 141 minutes 48.93 seconds (8508.93 seconds total)