Starting phenix.real_space_refine on Sat May 10 04:28:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.map" model { file = "/net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2g_35949/05_2025/8j2g_35949.cif" } resolution = 3.4 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= 0.010 sd= 0.143 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 42 5.16 5 C 3282 2.51 5 N 860 2.21 5 O 874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5058 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2529 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 4.25, per 1000 atoms: 0.84 Number of scatterers: 5058 At special positions: 0 Unit cell: (73.7, 67.1, 126.5, 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 42 16.00 O 874 8.00 N 860 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 636.7 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 45.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.658A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 46 " --> pdb=" O HIS A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.905A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.591A pdb=" N VAL A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.859A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.540A pdb=" N VAL A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.521A pdb=" N LEU A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.628A pdb=" N LEU A 314 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.094A pdb=" N TYR A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.579A pdb=" N ASN A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'B' and resid 11 through 32 removed outlier: 3.659A pdb=" N LEU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.904A pdb=" N GLU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.592A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.858A pdb=" N ILE B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.539A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.964A pdb=" N LEU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.522A pdb=" N LEU B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.627A pdb=" N LEU B 314 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 322 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.093A pdb=" N TYR B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.580A pdb=" N ASN B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1588 1.34 - 1.46: 950 1.46 - 1.58: 2572 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 5172 Sorted by residual: bond pdb=" CA HIS B 251 " pdb=" C HIS B 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA HIS A 251 " pdb=" C HIS A 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.34e+00 bond pdb=" CB PRO B 318 " pdb=" CG PRO B 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.29e+00 bond pdb=" CB VAL B 248 " pdb=" CG1 VAL B 248 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 5167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 6688 2.37 - 4.73: 298 4.73 - 7.10: 38 7.10 - 9.46: 6 9.46 - 11.83: 4 Bond angle restraints: 7034 Sorted by residual: angle pdb=" N ARG B 246 " pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 114.64 102.81 11.83 1.52e+00 4.33e-01 6.06e+01 angle pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 114.64 102.86 11.78 1.52e+00 4.33e-01 6.01e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 114.12 108.34 5.78 1.39e+00 5.18e-01 1.73e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 114.12 108.39 5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C PHE A 134 " pdb=" N HIS A 135 " pdb=" CA HIS A 135 " ideal model delta sigma weight residual 120.82 126.73 -5.91 1.47e+00 4.63e-01 1.62e+01 ... (remaining 7029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.99: 2399 7.99 - 15.99: 455 15.99 - 23.98: 117 23.98 - 31.98: 39 31.98 - 39.97: 30 Dihedral angle restraints: 3040 sinusoidal: 1166 harmonic: 1874 Sorted by residual: dihedral pdb=" CA ASN B 299 " pdb=" C ASN B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual -180.00 -147.46 -32.54 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA VAL B 128 " pdb=" C VAL B 128 " pdb=" N LEU B 129 " pdb=" CA LEU B 129 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 363 0.036 - 0.073: 335 0.073 - 0.109: 98 0.109 - 0.145: 27 0.145 - 0.182: 15 Chirality restraints: 838 Sorted by residual: chirality pdb=" CA PRO A 318 " pdb=" N PRO A 318 " pdb=" C PRO A 318 " pdb=" CB PRO A 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA PRO B 318 " pdb=" N PRO B 318 " pdb=" C PRO B 318 " pdb=" CB PRO B 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 835 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 317 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 318 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 317 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 318 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 333 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 334 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.035 5.00e-02 4.00e+02 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1797 2.88 - 3.39: 4412 3.39 - 3.89: 7453 3.89 - 4.40: 8331 4.40 - 4.90: 14363 Nonbonded interactions: 36356 Sorted by model distance: nonbonded pdb=" OE2 GLU B 109 " pdb=" NE1 TRP B 273 " model vdw 2.380 3.120 nonbonded pdb=" OE2 GLU A 109 " pdb=" NE1 TRP A 273 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLN B 376 " pdb=" O GLY B 379 " model vdw 2.382 3.120 nonbonded pdb=" NE2 GLN A 376 " pdb=" O GLY A 379 " model vdw 2.382 3.120 nonbonded pdb=" O GLU B 58 " pdb=" NH1 ARG B 62 " model vdw 2.390 3.120 ... (remaining 36351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.490 Find NCS groups from input model: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.010 0.104 5174 Z= 0.395 Angle : 1.138 11.829 7038 Z= 0.625 Chirality : 0.057 0.182 838 Planarity : 0.008 0.072 878 Dihedral : 10.183 38.574 1818 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.39 (0.24), residues: 642 helix: -5.04 (0.09), residues: 350 sheet: -1.22 (0.89), residues: 46 loop : -3.27 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 375 HIS 0.008 0.002 HIS B 373 PHE 0.022 0.003 PHE A 407 TYR 0.012 0.003 TYR B 270 ARG 0.011 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.31674 ( 128) hydrogen bonds : angle 9.51772 ( 372) SS BOND : bond 0.00222 ( 2) SS BOND : angle 1.20899 ( 4) covalent geometry : bond 0.00958 ( 5172) covalent geometry : angle 1.13802 ( 7034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: A 99 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 64 THR cc_start: 0.8794 (p) cc_final: 0.8353 (m) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1614 time to fit residues: 20.8836 Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 370 HIS A 409 ASN A 413 HIS B 251 HIS B 284 ASN B 370 HIS B 409 ASN B 413 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.191153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139626 restraints weight = 5617.659| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.62 r_work: 0.3485 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5174 Z= 0.150 Angle : 0.725 20.014 7038 Z= 0.350 Chirality : 0.042 0.141 838 Planarity : 0.006 0.054 878 Dihedral : 7.243 29.655 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.91 % Allowed : 8.15 % Favored : 90.94 % 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: -5.54 (0.26), residues: 642 helix: -4.25 (0.16), residues: 354 sheet: -1.36 (0.80), residues: 46 loop : -2.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 375 HIS 0.003 0.001 HIS B 373 PHE 0.012 0.001 PHE B 94 TYR 0.016 0.002 TYR B 270 ARG 0.002 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 128) hydrogen bonds : angle 5.56496 ( 372) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.06330 ( 4) covalent geometry : bond 0.00359 ( 5172) covalent geometry : angle 0.72487 ( 7034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7890 (ttm-80) REVERT: A 44 MET cc_start: 0.8059 (mtp) cc_final: 0.7825 (mtt) REVERT: A 78 GLU cc_start: 0.8640 (pt0) cc_final: 0.8257 (pt0) REVERT: A 99 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 44 MET cc_start: 0.8230 (mtm) cc_final: 0.7995 (mtt) REVERT: B 78 GLU cc_start: 0.8553 (pt0) cc_final: 0.8200 (pt0) REVERT: B 80 MET cc_start: 0.8939 (ptm) cc_final: 0.8575 (ptm) REVERT: B 99 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 371 GLU cc_start: 0.8300 (tp30) cc_final: 0.7937 (tp30) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.1236 time to fit residues: 15.0661 Evaluate side-chains 74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.188594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135808 restraints weight = 5760.518| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.74 r_work: 0.3372 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5174 Z= 0.203 Angle : 0.753 20.766 7038 Z= 0.358 Chirality : 0.044 0.137 838 Planarity : 0.005 0.054 878 Dihedral : 7.065 28.732 686 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.63 % Allowed : 11.05 % Favored : 87.32 % 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: -4.91 (0.29), residues: 642 helix: -3.71 (0.20), residues: 354 sheet: -1.08 (0.81), residues: 46 loop : -2.65 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 375 HIS 0.005 0.001 HIS A 373 PHE 0.014 0.002 PHE A 94 TYR 0.025 0.003 TYR B 270 ARG 0.003 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 128) hydrogen bonds : angle 4.92914 ( 372) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.85808 ( 4) covalent geometry : bond 0.00496 ( 5172) covalent geometry : angle 0.75253 ( 7034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7977 (ttm-80) REVERT: A 44 MET cc_start: 0.8188 (mtp) cc_final: 0.7951 (mtt) REVERT: A 99 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 359 GLU cc_start: 0.7894 (mp0) cc_final: 0.7430 (mp0) REVERT: B 44 MET cc_start: 0.8375 (mtm) cc_final: 0.8129 (mtt) REVERT: B 99 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7365 (tm-30) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.1723 time to fit residues: 20.2880 Evaluate side-chains 80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.189184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133839 restraints weight = 5660.336| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.09 r_work: 0.3425 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5174 Z= 0.105 Angle : 0.642 19.386 7038 Z= 0.304 Chirality : 0.041 0.133 838 Planarity : 0.004 0.034 878 Dihedral : 6.301 27.272 686 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.54 % Allowed : 11.78 % Favored : 87.68 % 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: -4.44 (0.30), residues: 642 helix: -3.28 (0.23), residues: 352 sheet: -0.88 (0.80), residues: 46 loop : -2.55 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.002 TYR B 270 ARG 0.001 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 128) hydrogen bonds : angle 4.35462 ( 372) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.69495 ( 4) covalent geometry : bond 0.00250 ( 5172) covalent geometry : angle 0.64172 ( 7034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.8009 (ttm-80) REVERT: A 20 MET cc_start: 0.7868 (ppp) cc_final: 0.7576 (ppp) REVERT: A 58 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 78 GLU cc_start: 0.8630 (pt0) cc_final: 0.8257 (pt0) REVERT: A 99 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 125 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7795 (tp) REVERT: B 10 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8419 (mtm-85) REVERT: B 30 ARG cc_start: 0.7069 (tmt170) cc_final: 0.6611 (tmt170) REVERT: B 44 MET cc_start: 0.8220 (mtm) cc_final: 0.7939 (mtt) REVERT: B 58 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 78 GLU cc_start: 0.8575 (pt0) cc_final: 0.8268 (pt0) REVERT: B 80 MET cc_start: 0.8882 (ptm) cc_final: 0.8507 (ptm) outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.2150 time to fit residues: 21.1606 Evaluate side-chains 72 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 332 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134301 restraints weight = 5492.740| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.82 r_work: 0.3455 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5174 Z= 0.087 Angle : 0.596 18.021 7038 Z= 0.281 Chirality : 0.040 0.133 838 Planarity : 0.004 0.031 878 Dihedral : 5.698 25.747 686 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.63 % Allowed : 11.96 % Favored : 86.41 % 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: -4.25 (0.30), residues: 642 helix: -3.03 (0.23), residues: 362 sheet: -0.35 (0.80), residues: 46 loop : -2.70 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.000 HIS A 43 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.001 TYR B 270 ARG 0.003 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02548 ( 128) hydrogen bonds : angle 3.96357 ( 372) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.58935 ( 4) covalent geometry : bond 0.00202 ( 5172) covalent geometry : angle 0.59614 ( 7034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7910 (ttm-80) REVERT: A 30 ARG cc_start: 0.7138 (tmt170) cc_final: 0.6740 (tmt170) REVERT: A 58 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 78 GLU cc_start: 0.8663 (pt0) cc_final: 0.8410 (pt0) REVERT: A 99 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 10 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8379 (mtm-85) REVERT: B 30 ARG cc_start: 0.7023 (tmt170) cc_final: 0.6679 (tmt170) REVERT: B 78 GLU cc_start: 0.8652 (pt0) cc_final: 0.8325 (pt0) REVERT: B 80 MET cc_start: 0.8813 (ptm) cc_final: 0.8546 (ptm) REVERT: B 388 ILE cc_start: 0.7748 (mt) cc_final: 0.7338 (pt) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.1765 time to fit residues: 18.8062 Evaluate side-chains 70 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.190784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132309 restraints weight = 5452.082| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.85 r_work: 0.3434 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5174 Z= 0.102 Angle : 0.616 18.183 7038 Z= 0.285 Chirality : 0.041 0.133 838 Planarity : 0.004 0.032 878 Dihedral : 5.615 24.684 686 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.17 % Allowed : 12.68 % Favored : 85.14 % 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: -3.75 (0.31), residues: 642 helix: -2.73 (0.25), residues: 354 sheet: 0.17 (0.84), residues: 46 loop : -2.39 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.009 0.001 PHE B 21 TYR 0.012 0.001 TYR B 270 ARG 0.003 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 128) hydrogen bonds : angle 3.84050 ( 372) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.56768 ( 4) covalent geometry : bond 0.00243 ( 5172) covalent geometry : angle 0.61590 ( 7034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7914 (ttm-80) REVERT: A 20 MET cc_start: 0.7803 (ppp) cc_final: 0.7572 (ppp) REVERT: A 30 ARG cc_start: 0.6900 (tmt170) cc_final: 0.6465 (tmt170) REVERT: A 58 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 78 GLU cc_start: 0.8699 (pt0) cc_final: 0.8409 (pt0) REVERT: B 30 ARG cc_start: 0.7035 (tmt170) cc_final: 0.6690 (tmt170) REVERT: B 58 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 78 GLU cc_start: 0.8687 (pt0) cc_final: 0.8332 (pt0) REVERT: B 80 MET cc_start: 0.8761 (ptm) cc_final: 0.8473 (ptm) REVERT: B 388 ILE cc_start: 0.7686 (mt) cc_final: 0.7292 (pt) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1672 time to fit residues: 17.2096 Evaluate side-chains 68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 345 GLN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.187259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128317 restraints weight = 5480.830| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.88 r_work: 0.3362 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5174 Z= 0.149 Angle : 0.650 19.029 7038 Z= 0.304 Chirality : 0.042 0.134 838 Planarity : 0.004 0.033 878 Dihedral : 5.836 23.994 686 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.08 % Allowed : 13.41 % Favored : 83.51 % 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 (0.32), residues: 642 helix: -2.67 (0.25), residues: 354 sheet: 0.12 (0.83), residues: 46 loop : -2.31 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.004 0.001 HIS A 373 PHE 0.011 0.001 PHE A 94 TYR 0.012 0.001 TYR B 270 ARG 0.004 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 128) hydrogen bonds : angle 3.98561 ( 372) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.47661 ( 4) covalent geometry : bond 0.00364 ( 5172) covalent geometry : angle 0.64989 ( 7034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7641 (ttm-80) REVERT: A 30 ARG cc_start: 0.7014 (tmt170) cc_final: 0.6526 (tmt170) REVERT: A 78 GLU cc_start: 0.8710 (pt0) cc_final: 0.8251 (pt0) REVERT: A 125 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7888 (tp) REVERT: A 381 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6526 (ttt90) REVERT: B 30 ARG cc_start: 0.7197 (tmt170) cc_final: 0.6750 (tmt170) REVERT: B 359 GLU cc_start: 0.7395 (mp0) cc_final: 0.7090 (mt-10) REVERT: B 388 ILE cc_start: 0.7777 (mt) cc_final: 0.7352 (pt) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.1583 time to fit residues: 17.7929 Evaluate side-chains 85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 409 ASN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.184420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124930 restraints weight = 5618.843| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.92 r_work: 0.3354 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5174 Z= 0.197 Angle : 0.691 19.840 7038 Z= 0.324 Chirality : 0.044 0.135 838 Planarity : 0.004 0.034 878 Dihedral : 6.155 23.853 686 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.99 % Allowed : 13.59 % Favored : 82.43 % 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: -3.70 (0.32), residues: 642 helix: -2.73 (0.25), residues: 352 sheet: -0.11 (0.83), residues: 46 loop : -2.23 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.005 0.001 HIS B 43 PHE 0.013 0.001 PHE A 94 TYR 0.010 0.002 TYR B 270 ARG 0.004 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 128) hydrogen bonds : angle 4.20820 ( 372) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.45397 ( 4) covalent geometry : bond 0.00485 ( 5172) covalent geometry : angle 0.69100 ( 7034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7557 (ttm-80) REVERT: A 20 MET cc_start: 0.7721 (ppp) cc_final: 0.7496 (ppp) REVERT: A 80 MET cc_start: 0.8715 (ttm) cc_final: 0.8489 (tpp) REVERT: A 125 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 359 GLU cc_start: 0.7931 (mp0) cc_final: 0.7726 (mp0) REVERT: A 381 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6315 (ttt90) REVERT: B 30 ARG cc_start: 0.7167 (tmt170) cc_final: 0.6873 (tmt170) outliers start: 22 outliers final: 19 residues processed: 92 average time/residue: 0.1611 time to fit residues: 19.4089 Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.0370 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.191192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132599 restraints weight = 5484.299| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.88 r_work: 0.3450 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5174 Z= 0.084 Angle : 0.584 17.835 7038 Z= 0.274 Chirality : 0.040 0.129 838 Planarity : 0.003 0.030 878 Dihedral : 5.341 22.466 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.63 % Allowed : 16.30 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.52 (0.32), residues: 642 helix: -2.37 (0.26), residues: 364 sheet: 0.19 (0.85), residues: 46 loop : -2.57 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 375 HIS 0.002 0.000 HIS B 108 PHE 0.007 0.001 PHE B 21 TYR 0.009 0.001 TYR B 270 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.02355 ( 128) hydrogen bonds : angle 3.73924 ( 372) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.48761 ( 4) covalent geometry : bond 0.00192 ( 5172) covalent geometry : angle 0.58389 ( 7034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7546 (ttm-80) REVERT: A 20 MET cc_start: 0.7647 (ppp) cc_final: 0.7445 (ppp) REVERT: B 78 GLU cc_start: 0.8545 (pt0) cc_final: 0.8207 (pt0) REVERT: B 80 MET cc_start: 0.8789 (ptm) cc_final: 0.8262 (ttp) REVERT: B 92 LEU cc_start: 0.8117 (tp) cc_final: 0.7882 (tt) REVERT: B 388 ILE cc_start: 0.7773 (mt) cc_final: 0.7358 (pt) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.1528 time to fit residues: 15.1858 Evaluate side-chains 64 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.0030 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.192345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133956 restraints weight = 5448.530| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.90 r_work: 0.3468 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5174 Z= 0.083 Angle : 0.589 17.482 7038 Z= 0.273 Chirality : 0.040 0.131 838 Planarity : 0.003 0.032 878 Dihedral : 5.111 21.403 686 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.27 % Allowed : 16.49 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.91 (0.33), residues: 642 helix: -2.01 (0.27), residues: 348 sheet: 0.53 (0.84), residues: 46 loop : -2.08 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 375 HIS 0.001 0.000 HIS B 43 PHE 0.008 0.001 PHE A 94 TYR 0.007 0.001 TYR B 270 ARG 0.001 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02246 ( 128) hydrogen bonds : angle 3.57406 ( 372) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.47370 ( 4) covalent geometry : bond 0.00195 ( 5172) covalent geometry : angle 0.58956 ( 7034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7880 (ttp-170) cc_final: 0.7616 (ttm-80) REVERT: B 65 HIS cc_start: 0.8202 (m-70) cc_final: 0.7754 (t-90) REVERT: B 78 GLU cc_start: 0.8520 (pt0) cc_final: 0.8203 (pt0) REVERT: B 80 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8132 (ttp) REVERT: B 92 LEU cc_start: 0.8123 (tp) cc_final: 0.7891 (tt) REVERT: B 388 ILE cc_start: 0.7792 (mt) cc_final: 0.7423 (pt) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1751 time to fit residues: 14.8704 Evaluate side-chains 61 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.191360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134591 restraints weight = 5541.673| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.61 r_work: 0.3442 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5174 Z= 0.094 Angle : 0.597 17.741 7038 Z= 0.276 Chirality : 0.041 0.132 838 Planarity : 0.003 0.032 878 Dihedral : 5.059 20.803 686 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.45 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.74 (0.33), residues: 642 helix: -1.86 (0.28), residues: 348 sheet: 0.69 (0.84), residues: 46 loop : -2.05 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.002 0.000 HIS A 373 PHE 0.009 0.001 PHE A 94 TYR 0.014 0.001 TYR B 270 ARG 0.003 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02404 ( 128) hydrogen bonds : angle 3.56776 ( 372) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.46987 ( 4) covalent geometry : bond 0.00226 ( 5172) covalent geometry : angle 0.59750 ( 7034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2586.55 seconds wall clock time: 45 minutes 39.82 seconds (2739.82 seconds total)