Starting phenix.real_space_refine on Sat Jan 18 05:38:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdz_60018/01_2025/8zdz_60018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdz_60018/01_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_60018/01_2025/8zdz_60018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdz_60018/01_2025/8zdz_60018.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdz_60018/01_2025/8zdz_60018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdz_60018/01_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-5571/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: 5.84, per 1000 atoms: 0.49 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: 3.07 Conformation dependent library (CDL) restraints added in 1.7 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: 0.90 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: 3.63 Time building geometry restraints manager: 3.55 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: 0.590 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: 0.090 Set scattering table: 0.120 Process input model: 27.180 Find NCS groups from input model: 0.260 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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= 0.238 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 *********************** 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 : 1.352 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: 0.8126 time to fit residues: 242.1871 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 : 1.421 ------------------------------------------------------------------------------- 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 = 19348.036| |-----------------------------------------------------------------------------| 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: 0.7944 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= 0.250 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 *********************** 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 : 1.404 Fit side-chains REVERT: A 51 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7881 (mpt) REVERT: A 123 ASN cc_start: 0.7549 (m-40) cc_final: 0.7265 (p0) REVERT: A 159 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8358 (pp30) REVERT: A 318 MET cc_start: 0.6857 (tmm) cc_final: 0.6638 (tmm) REVERT: A 376 GLU cc_start: 0.8874 (tp30) cc_final: 0.8605 (tp30) REVERT: D 31 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6224 (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: 0.8172 (pp30) REVERT: D 376 GLU cc_start: 0.8861 (tp30) cc_final: 0.8534 (tm-30) REVERT: C 31 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6001 (tp40) REVERT: C 51 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7849 (mpt) REVERT: C 123 ASN cc_start: 0.7612 (m-40) cc_final: 0.7234 (p0) REVERT: C 159 GLN cc_start: 0.8688 (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: 0.6166 (tp40) REVERT: B 51 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7857 (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: 0.8785 time to fit residues: 229.2914 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 : 1.382 ------------------------------------------------------------------------------- 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: 0.9980 chunk 115 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070869 restraints weight = 19463.054| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.90 r_work: 0.2709 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12256 Z= 0.219 Angle : 0.555 8.596 16588 Z= 0.279 Chirality : 0.037 0.145 1968 Planarity : 0.003 0.030 2008 Dihedral : 4.446 56.549 1644 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.45 % Allowed : 30.53 % Favored : 64.02 % 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: 3.53 (0.21), residues: 1472 helix: 3.14 (0.14), residues: 1228 sheet: -1.42 (0.65), residues: 48 loop : -2.44 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.002 0.001 HIS C 189 PHE 0.008 0.001 PHE D 291 TYR 0.013 0.001 TYR A 214 ARG 0.002 0.000 ARG D 340 *********************** 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: 72 poor density : 178 time to evaluate : 1.549 Fit side-chains REVERT: A 51 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7891 (mpt) REVERT: A 85 SER cc_start: 0.8887 (p) cc_final: 0.8650 (m) REVERT: A 159 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8369 (pp30) REVERT: A 318 MET cc_start: 0.6891 (tmm) cc_final: 0.6656 (tmm) REVERT: A 323 ASP cc_start: 0.5963 (t70) cc_final: 0.5560 (p0) REVERT: A 376 GLU cc_start: 0.8907 (tp30) cc_final: 0.8520 (tp30) REVERT: D 51 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7901 (mpt) REVERT: D 85 SER cc_start: 0.8880 (p) cc_final: 0.8625 (m) REVERT: D 376 GLU cc_start: 0.8914 (tp30) cc_final: 0.8576 (tm-30) REVERT: C 51 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7830 (mpt) REVERT: C 85 SER cc_start: 0.8885 (p) cc_final: 0.8637 (m) REVERT: C 123 ASN cc_start: 0.7648 (m-40) cc_final: 0.7195 (p0) REVERT: C 279 GLU cc_start: 0.8696 (tt0) cc_final: 0.8411 (tt0) REVERT: C 376 GLU cc_start: 0.8920 (tp30) cc_final: 0.8641 (tp30) REVERT: C 379 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8899 (tppp) REVERT: B 51 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7879 (mpt) REVERT: B 85 SER cc_start: 0.8870 (p) cc_final: 0.8620 (m) REVERT: B 376 GLU cc_start: 0.8929 (tp30) cc_final: 0.8550 (tp30) outliers start: 72 outliers final: 19 residues processed: 228 average time/residue: 0.8912 time to fit residues: 228.1295 Evaluate side-chains 205 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 388 ASP 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 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 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 271 ILE Chi-restraints excluded: chain B residue 374 LEU 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 23 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 171 ASN A 421 GLN D 171 ASN D 421 GLN 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 = 0.3408 r_free = 0.3408 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067811 restraints weight = 19222.756| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.85 r_work: 0.2654 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12256 Z= 0.333 Angle : 0.611 8.232 16588 Z= 0.304 Chirality : 0.039 0.146 1968 Planarity : 0.003 0.024 2008 Dihedral : 4.167 46.703 1644 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.83 % Allowed : 29.85 % Favored : 64.32 % 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: 3.51 (0.22), residues: 1472 helix: 3.12 (0.14), residues: 1228 sheet: -1.29 (0.68), residues: 48 loop : -2.45 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 154 HIS 0.004 0.001 HIS D 306 PHE 0.011 0.001 PHE A 370 TYR 0.013 0.001 TYR A 214 ARG 0.003 0.000 ARG A 340 *********************** 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 244 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 1.492 Fit side-chains REVERT: A 51 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7986 (mpt) REVERT: A 376 GLU cc_start: 0.8980 (tp30) cc_final: 0.8667 (tp30) REVERT: A 379 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8894 (tppp) REVERT: D 51 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7904 (mpt) REVERT: D 376 GLU cc_start: 0.8969 (tp30) cc_final: 0.8552 (tm-30) REVERT: C 51 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7922 (mpt) REVERT: C 279 GLU cc_start: 0.8784 (tt0) cc_final: 0.8495 (tt0) REVERT: C 376 GLU cc_start: 0.8978 (tp30) cc_final: 0.8703 (tp30) REVERT: C 379 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8886 (tppp) REVERT: B 51 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7944 (mpt) REVERT: B 376 GLU cc_start: 0.9002 (tp30) cc_final: 0.8522 (tm-30) outliers start: 77 outliers final: 20 residues processed: 226 average time/residue: 0.8485 time to fit residues: 215.8008 Evaluate side-chains 175 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 A residue 388 ASP 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 51 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 86 VAL 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 151 VAL Chi-restraints excluded: chain B residue 271 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: 6.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.104941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.072278 restraints weight = 19304.737| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.84 r_work: 0.2716 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2349 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= 0.180 Angle : 0.574 8.641 16588 Z= 0.280 Chirality : 0.037 0.145 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.790 31.563 1644 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.02 % Allowed : 32.35 % 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: 3.73 (0.22), residues: 1472 helix: 3.24 (0.14), residues: 1232 sheet: -1.17 (0.66), residues: 48 loop : -2.32 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS D 306 PHE 0.006 0.001 PHE B 291 TYR 0.012 0.001 TYR A 292 ARG 0.001 0.000 ARG A 340 *********************** 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 208 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 1.373 Fit side-chains REVERT: A 376 GLU cc_start: 0.8970 (tp30) cc_final: 0.8495 (tm-30) REVERT: A 421 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8183 (pp30) REVERT: D 51 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7897 (mpt) REVERT: D 376 GLU cc_start: 0.8990 (tp30) cc_final: 0.8567 (tm-30) REVERT: D 421 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8177 (pp30) REVERT: C 51 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7872 (mpt) REVERT: C 279 GLU cc_start: 0.8719 (tt0) cc_final: 0.8433 (tt0) REVERT: C 376 GLU cc_start: 0.8990 (tp30) cc_final: 0.8658 (tp30) REVERT: C 422 PHE cc_start: 0.7946 (t80) cc_final: 0.7709 (t80) REVERT: B 376 GLU cc_start: 0.8991 (tp30) cc_final: 0.8520 (tm-30) REVERT: B 421 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8272 (pp30) outliers start: 53 outliers final: 21 residues processed: 195 average time/residue: 0.9784 time to fit residues: 211.9976 Evaluate side-chains 185 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 A residue 388 ASP 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 86 VAL 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 51 MET 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 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: 4.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 330 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 = 0.3474 r_free = 0.3474 target = 0.105749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.072882 restraints weight = 19439.058| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.88 r_work: 0.2752 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2450 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= 0.160 Angle : 0.570 9.034 16588 Z= 0.282 Chirality : 0.036 0.150 1968 Planarity : 0.003 0.023 2008 Dihedral : 3.685 26.212 1644 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.03 % Allowed : 32.88 % 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 (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: 3.32 (0.14), residues: 1232 sheet: -1.16 (0.65), residues: 48 loop : -2.22 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 154 HIS 0.004 0.001 HIS A 306 PHE 0.031 0.001 PHE B 422 TYR 0.011 0.001 TYR B 292 ARG 0.001 0.000 ARG C 272 *********************** 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 204 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 1.387 Fit side-chains REVERT: A 376 GLU cc_start: 0.8984 (tp30) cc_final: 0.8504 (tm-30) REVERT: D 51 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7896 (mpt) REVERT: D 376 GLU cc_start: 0.8985 (tp30) cc_final: 0.8542 (tm-30) REVERT: D 421 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7989 (pp30) REVERT: C 279 GLU cc_start: 0.8715 (tt0) cc_final: 0.8428 (tt0) REVERT: C 376 GLU cc_start: 0.8984 (tp30) cc_final: 0.8536 (tm-30) REVERT: B 376 GLU cc_start: 0.8986 (tp30) cc_final: 0.8500 (tm-30) REVERT: B 421 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8093 (pp30) outliers start: 40 outliers final: 12 residues processed: 188 average time/residue: 0.9131 time to fit residues: 192.2956 Evaluate side-chains 169 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain C residue 145 ILE 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 145 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 421 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.106090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.073365 restraints weight = 19222.026| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.86 r_work: 0.2752 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2529 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= 0.167 Angle : 0.594 9.764 16588 Z= 0.290 Chirality : 0.037 0.147 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.418 14.257 1640 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.48 % Allowed : 32.42 % 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 (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: -1.46 (0.60), residues: 48 loop : -2.12 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 154 HIS 0.004 0.001 HIS A 306 PHE 0.017 0.001 PHE B 422 TYR 0.010 0.001 TYR A 214 ARG 0.001 0.000 ARG D 340 *********************** 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 202 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.471 Fit side-chains REVERT: A 83 ASP cc_start: 0.7874 (t0) cc_final: 0.7547 (t0) REVERT: A 376 GLU cc_start: 0.8988 (tp30) cc_final: 0.8491 (tm-30) REVERT: D 51 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7888 (mpt) REVERT: D 83 ASP cc_start: 0.7869 (t0) cc_final: 0.7560 (t0) REVERT: D 376 GLU cc_start: 0.8998 (tp30) cc_final: 0.8539 (tm-30) REVERT: C 83 ASP cc_start: 0.7869 (t0) cc_final: 0.7562 (t0) REVERT: C 279 GLU cc_start: 0.8686 (tt0) cc_final: 0.8399 (tt0) REVERT: C 376 GLU cc_start: 0.8981 (tp30) cc_final: 0.8516 (tm-30) REVERT: B 376 GLU cc_start: 0.8998 (tp30) cc_final: 0.8497 (tm-30) outliers start: 46 outliers final: 19 residues processed: 189 average time/residue: 0.9649 time to fit residues: 203.9324 Evaluate side-chains 177 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 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 69 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 145 ILE 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 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 194 ASN C 421 GLN B 194 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 = 0.3502 r_free = 0.3502 target = 0.107703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074950 restraints weight = 19491.822| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.88 r_work: 0.2765 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2602 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= 0.167 Angle : 0.617 10.678 16588 Z= 0.304 Chirality : 0.037 0.155 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.471 19.400 1640 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.73 % Allowed : 33.56 % Favored : 63.71 % 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: 3.98 (0.22), residues: 1472 helix: 3.41 (0.14), residues: 1232 sheet: -1.60 (0.59), residues: 48 loop : -2.05 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.004 0.001 HIS B 306 PHE 0.032 0.001 PHE A 422 TYR 0.009 0.001 TYR A 292 ARG 0.001 0.000 ARG B 272 *********************** 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 192 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.486 Fit side-chains REVERT: A 51 MET cc_start: 0.8646 (tpp) cc_final: 0.8355 (mmt) REVERT: A 83 ASP cc_start: 0.7809 (t0) cc_final: 0.7577 (t0) REVERT: A 123 ASN cc_start: 0.7390 (m-40) cc_final: 0.6878 (p0) REVERT: A 376 GLU cc_start: 0.8985 (tp30) cc_final: 0.8507 (tm-30) REVERT: A 421 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8120 (pp30) REVERT: D 51 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7866 (mpt) REVERT: D 83 ASP cc_start: 0.7840 (t0) cc_final: 0.7620 (t0) REVERT: D 376 GLU cc_start: 0.9033 (tp30) cc_final: 0.8617 (tm-30) REVERT: C 51 MET cc_start: 0.8671 (tpp) cc_final: 0.8282 (mmt) REVERT: C 83 ASP cc_start: 0.7812 (t0) cc_final: 0.7598 (t0) REVERT: C 279 GLU cc_start: 0.8637 (tt0) cc_final: 0.8392 (tt0) REVERT: C 376 GLU cc_start: 0.8987 (tp30) cc_final: 0.8545 (tm-30) REVERT: B 83 ASP cc_start: 0.7834 (t0) cc_final: 0.7546 (t0) REVERT: B 376 GLU cc_start: 0.8999 (tp30) cc_final: 0.8523 (tm-30) outliers start: 36 outliers final: 21 residues processed: 183 average time/residue: 0.9678 time to fit residues: 197.9339 Evaluate side-chains 176 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 29 LYS 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 A residue 421 GLN Chi-restraints excluded: chain D residue 51 MET 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 69 VAL 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 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 374 LEU Chi-restraints excluded: chain B residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.107259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074381 restraints weight = 19222.521| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.90 r_work: 0.2762 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2653 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= 0.176 Angle : 0.642 10.930 16588 Z= 0.313 Chirality : 0.037 0.159 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.457 19.308 1640 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 34.02 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.02 (0.22), residues: 1472 helix: 3.44 (0.13), residues: 1232 sheet: -1.63 (0.57), residues: 48 loop : -2.01 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 154 HIS 0.003 0.001 HIS B 306 PHE 0.033 0.001 PHE B 422 TYR 0.009 0.001 TYR A 292 ARG 0.002 0.000 ARG A 36 *********************** 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 179 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.385 Fit side-chains REVERT: A 99 MET cc_start: 0.9208 (mmm) cc_final: 0.8982 (mmm) REVERT: A 376 GLU cc_start: 0.8982 (tp30) cc_final: 0.8498 (tm-30) REVERT: D 51 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7879 (mpt) REVERT: D 376 GLU cc_start: 0.9021 (tp30) cc_final: 0.8602 (tm-30) REVERT: C 279 GLU cc_start: 0.8643 (tt0) cc_final: 0.8381 (tt0) REVERT: C 376 GLU cc_start: 0.8971 (tp30) cc_final: 0.8518 (tm-30) REVERT: B 51 MET cc_start: 0.8671 (tpp) cc_final: 0.8306 (mmt) REVERT: B 83 ASP cc_start: 0.7817 (t0) cc_final: 0.7579 (t0) REVERT: B 376 GLU cc_start: 0.9001 (tp30) cc_final: 0.8520 (tm-30) outliers start: 29 outliers final: 21 residues processed: 170 average time/residue: 0.9711 time to fit residues: 183.9060 Evaluate side-chains 174 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 29 LYS 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 51 MET 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 69 VAL 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 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 374 LEU Chi-restraints excluded: chain B residue 421 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 39 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 266 ASN 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 = 0.3461 r_free = 0.3461 target = 0.105243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072146 restraints weight = 19355.129| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.88 r_work: 0.2725 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12256 Z= 0.227 Angle : 0.660 11.424 16588 Z= 0.325 Chirality : 0.038 0.156 1968 Planarity : 0.003 0.023 2008 Dihedral : 3.438 19.066 1640 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.97 % Allowed : 34.24 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.97 (0.22), residues: 1472 helix: 3.40 (0.13), residues: 1232 sheet: -1.62 (0.58), residues: 48 loop : -2.04 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.004 0.001 HIS B 306 PHE 0.034 0.001 PHE A 422 TYR 0.010 0.001 TYR A 292 ARG 0.003 0.000 ARG B 340 ********************** 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 181 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.353 Fit side-chains REVERT: A 51 MET cc_start: 0.8719 (tpp) cc_final: 0.8281 (mmt) REVERT: A 99 MET cc_start: 0.9213 (mmm) cc_final: 0.8891 (mmm) REVERT: A 376 GLU cc_start: 0.8991 (tp30) cc_final: 0.8491 (tm-30) REVERT: D 51 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7894 (mpt) REVERT: D 376 GLU cc_start: 0.9036 (tp30) cc_final: 0.8612 (tm-30) REVERT: C 279 GLU cc_start: 0.8686 (tt0) cc_final: 0.8451 (tt0) REVERT: C 376 GLU cc_start: 0.8984 (tp30) cc_final: 0.8524 (tm-30) REVERT: B 51 MET cc_start: 0.8678 (tpp) cc_final: 0.8375 (mmt) REVERT: B 83 ASP cc_start: 0.7906 (t0) cc_final: 0.7636 (t0) REVERT: B 376 GLU cc_start: 0.9006 (tp30) cc_final: 0.8508 (tm-30) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.9451 time to fit residues: 185.8011 Evaluate side-chains 171 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 A residue 421 GLN Chi-restraints excluded: chain D residue 51 MET 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 69 VAL 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 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 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.106833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073753 restraints weight = 19150.452| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.89 r_work: 0.2761 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2713 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= 0.174 Angle : 0.649 11.486 16588 Z= 0.317 Chirality : 0.037 0.156 1968 Planarity : 0.003 0.024 2008 Dihedral : 3.459 19.354 1640 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.89 % Allowed : 34.02 % 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 (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: 4.02 (0.22), residues: 1472 helix: 3.43 (0.13), residues: 1232 sheet: -1.63 (0.57), residues: 48 loop : -1.99 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.004 0.001 HIS B 306 PHE 0.035 0.001 PHE B 422 TYR 0.009 0.001 TYR A 292 ARG 0.001 0.000 ARG D 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6950.16 seconds wall clock time: 124 minutes 56.05 seconds (7496.05 seconds total)