Starting phenix.real_space_refine on Fri Oct 10 12:31:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2g_35949/10_2025/8j2g_35949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2g_35949/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j2g_35949/10_2025/8j2g_35949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2g_35949/10_2025/8j2g_35949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j2g_35949/10_2025/8j2g_35949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2g_35949/10_2025/8j2g_35949.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.24, per 1000 atoms: 0.25 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: 0.23 Conformation dependent library (CDL) restraints added in 117.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.10 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: 0.45 Time building geometry restraints manager: 0.31 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: 0.01 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: 0.510 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 4.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.650 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.011 0.001 ARG A 76 TYR 0.012 0.003 TYR B 270 PHE 0.022 0.003 PHE A 407 TRP 0.015 0.003 TRP B 375 HIS 0.008 0.002 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00958 ( 5172) covalent geometry : angle 1.13802 ( 7034) SS BOND : bond 0.00222 ( 2) SS BOND : angle 1.20899 ( 4) hydrogen bonds : bond 0.31674 ( 128) hydrogen bonds : angle 9.51772 ( 372) *********************** 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 : 0.199 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: 0.0683 time to fit residues: 8.9082 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 : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.196862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143831 restraints weight = 5608.825| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.90 r_work: 0.3528 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 5174 Z= 0.105 Angle : 0.675 18.897 7038 Z= 0.327 Chirality : 0.040 0.141 838 Planarity : 0.005 0.048 878 Dihedral : 6.849 28.923 686 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.09 % Allowed : 7.43 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.72 (0.25), residues: 642 helix: -4.25 (0.15), residues: 364 sheet: -1.41 (0.79), residues: 46 loop : -3.16 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 10 TYR 0.015 0.001 TYR B 270 PHE 0.010 0.001 PHE B 94 TRP 0.017 0.001 TRP B 375 HIS 0.002 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5172) covalent geometry : angle 0.67431 ( 7034) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.09433 ( 4) hydrogen bonds : bond 0.03654 ( 128) hydrogen bonds : angle 5.49124 ( 372) *********************** 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 100 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7887 (ttm-80) REVERT: A 58 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 78 GLU cc_start: 0.8591 (pt0) cc_final: 0.8388 (pt0) REVERT: A 99 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 44 MET cc_start: 0.8106 (mtm) cc_final: 0.7770 (mtt) REVERT: B 58 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7512 (tp30) REVERT: B 80 MET cc_start: 0.8688 (ptm) cc_final: 0.8293 (ptm) REVERT: B 99 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7186 (tm-30) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 0.0582 time to fit residues: 7.7161 Evaluate side-chains 77 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain B residue 28 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 255 ASN B 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.192691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139178 restraints weight = 5612.151| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.82 r_work: 0.3496 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5174 Z= 0.129 Angle : 0.673 19.032 7038 Z= 0.320 Chirality : 0.042 0.143 838 Planarity : 0.004 0.035 878 Dihedral : 6.452 27.808 686 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.09 % Allowed : 11.05 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.69 (0.29), residues: 642 helix: -3.52 (0.21), residues: 352 sheet: -0.81 (0.80), residues: 46 loop : -2.65 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.024 0.002 TYR A 270 PHE 0.010 0.001 PHE A 94 TRP 0.014 0.001 TRP B 375 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5172) covalent geometry : angle 0.67291 ( 7034) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.86668 ( 4) hydrogen bonds : bond 0.03546 ( 128) hydrogen bonds : angle 4.66772 ( 372) *********************** 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 79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.7902 (ttm-80) REVERT: A 58 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 78 GLU cc_start: 0.8629 (pt0) cc_final: 0.8342 (pt0) REVERT: A 99 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 78 GLU cc_start: 0.8701 (pt0) cc_final: 0.8369 (pp20) REVERT: B 80 MET cc_start: 0.8897 (ptm) cc_final: 0.8456 (ptm) REVERT: B 99 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 371 GLU cc_start: 0.8296 (tp30) cc_final: 0.7895 (tp30) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.0589 time to fit residues: 6.2365 Evaluate side-chains 75 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7722 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.193586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140123 restraints weight = 5587.108| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.79 r_work: 0.3472 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5174 Z= 0.110 Angle : 0.626 18.563 7038 Z= 0.296 Chirality : 0.041 0.134 838 Planarity : 0.004 0.032 878 Dihedral : 6.016 26.414 686 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.45 % Allowed : 12.86 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.30), residues: 642 helix: -3.14 (0.23), residues: 352 sheet: -0.46 (0.80), residues: 46 loop : -2.56 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.017 0.002 TYR A 270 PHE 0.009 0.001 PHE A 94 TRP 0.010 0.001 TRP B 375 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5172) covalent geometry : angle 0.62618 ( 7034) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.70482 ( 4) hydrogen bonds : bond 0.02960 ( 128) hydrogen bonds : angle 4.27595 ( 372) *********************** 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 80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8321 (ttp-170) cc_final: 0.7940 (ttm-80) REVERT: A 58 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 78 GLU cc_start: 0.8583 (pt0) cc_final: 0.8302 (pt0) REVERT: A 99 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 30 ARG cc_start: 0.6858 (tmt170) cc_final: 0.6590 (tmt170) REVERT: B 58 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 78 GLU cc_start: 0.8696 (pt0) cc_final: 0.8407 (pp20) REVERT: B 80 MET cc_start: 0.8826 (ptm) cc_final: 0.8476 (ptm) REVERT: B 338 GLU cc_start: 0.8061 (tt0) cc_final: 0.7815 (tt0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.0679 time to fit residues: 7.1425 Evaluate side-chains 71 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 383 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.191383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133222 restraints weight = 5549.533| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.83 r_work: 0.3453 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3310 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= 0.098 Angle : 0.601 17.915 7038 Z= 0.284 Chirality : 0.041 0.133 838 Planarity : 0.004 0.031 878 Dihedral : 5.687 25.363 686 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.81 % Allowed : 12.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.30), residues: 642 helix: -2.92 (0.24), residues: 362 sheet: -0.02 (0.82), residues: 46 loop : -2.68 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.014 0.001 TYR A 270 PHE 0.008 0.001 PHE A 94 TRP 0.009 0.001 TRP A 375 HIS 0.002 0.000 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5172) covalent geometry : angle 0.60067 ( 7034) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.50558 ( 4) hydrogen bonds : bond 0.02653 ( 128) hydrogen bonds : angle 4.00927 ( 372) *********************** 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 74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.7871 (ttm-80) REVERT: A 30 ARG cc_start: 0.6738 (tmt170) cc_final: 0.6474 (tmt170) REVERT: A 78 GLU cc_start: 0.8558 (pt0) cc_final: 0.8313 (pt0) REVERT: A 99 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 58 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 78 GLU cc_start: 0.8686 (pt0) cc_final: 0.8338 (pp20) REVERT: B 80 MET cc_start: 0.8795 (ptm) cc_final: 0.8385 (ptm) REVERT: B 338 GLU cc_start: 0.7974 (tt0) cc_final: 0.7724 (tt0) REVERT: B 388 ILE cc_start: 0.7710 (mt) cc_final: 0.7304 (pt) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.0576 time to fit residues: 5.7351 Evaluate side-chains 69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 383 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.193791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136670 restraints weight = 5473.605| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.73 r_work: 0.3497 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3574 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 : 0.589 17.318 7038 Z= 0.273 Chirality : 0.040 0.132 838 Planarity : 0.003 0.032 878 Dihedral : 5.332 24.003 686 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.63 % Allowed : 13.77 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.31), residues: 642 helix: -2.61 (0.25), residues: 366 sheet: 0.34 (0.83), residues: 46 loop : -2.81 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.011 0.001 TYR A 270 PHE 0.007 0.001 PHE B 21 TRP 0.008 0.001 TRP A 375 HIS 0.002 0.000 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 5172) covalent geometry : angle 0.58880 ( 7034) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.53453 ( 4) hydrogen bonds : bond 0.02329 ( 128) hydrogen bonds : angle 3.73349 ( 372) *********************** 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 71 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7869 (ttm-80) REVERT: A 25 GLU cc_start: 0.7793 (tt0) cc_final: 0.7378 (tt0) REVERT: B 10 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: B 58 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 78 GLU cc_start: 0.8625 (pt0) cc_final: 0.8343 (pp20) REVERT: B 80 MET cc_start: 0.8693 (ptm) cc_final: 0.8263 (ptm) REVERT: B 388 ILE cc_start: 0.7761 (mt) cc_final: 0.7394 (pt) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.0655 time to fit residues: 6.1764 Evaluate side-chains 63 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.189877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130635 restraints weight = 5521.486| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.86 r_work: 0.3416 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5174 Z= 0.131 Angle : 0.611 17.986 7038 Z= 0.285 Chirality : 0.042 0.134 838 Planarity : 0.003 0.032 878 Dihedral : 5.532 23.560 686 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.99 % Allowed : 12.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.32), residues: 642 helix: -2.46 (0.25), residues: 356 sheet: 0.43 (0.85), residues: 46 loop : -2.44 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.010 0.001 TYR A 270 PHE 0.009 0.001 PHE A 94 TRP 0.008 0.001 TRP B 375 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5172) covalent geometry : angle 0.61095 ( 7034) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.50906 ( 4) hydrogen bonds : bond 0.02904 ( 128) hydrogen bonds : angle 3.81574 ( 372) *********************** 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 75 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8306 (ttp-170) cc_final: 0.7906 (ttm-80) REVERT: A 30 ARG cc_start: 0.6833 (tmt170) cc_final: 0.6598 (tmt170) REVERT: A 381 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6639 (ttt90) REVERT: B 78 GLU cc_start: 0.8725 (pt0) cc_final: 0.8361 (pp20) REVERT: B 80 MET cc_start: 0.8813 (ptm) cc_final: 0.8294 (tmm) REVERT: B 338 GLU cc_start: 0.7987 (tt0) cc_final: 0.7743 (tt0) REVERT: B 345 GLN cc_start: 0.8055 (mt0) cc_final: 0.7765 (mt0) REVERT: B 388 ILE cc_start: 0.7737 (mt) cc_final: 0.7356 (pt) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.0688 time to fit residues: 6.8046 Evaluate side-chains 73 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU 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 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.188362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128949 restraints weight = 5548.786| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.88 r_work: 0.3395 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5174 Z= 0.140 Angle : 0.620 18.172 7038 Z= 0.290 Chirality : 0.042 0.134 838 Planarity : 0.004 0.031 878 Dihedral : 5.643 22.876 686 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.36 % Allowed : 12.68 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.33), residues: 642 helix: -2.33 (0.26), residues: 352 sheet: 0.35 (0.85), residues: 46 loop : -2.26 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.011 0.001 TYR A 270 PHE 0.010 0.001 PHE A 94 TRP 0.009 0.001 TRP B 375 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5172) covalent geometry : angle 0.62049 ( 7034) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.44809 ( 4) hydrogen bonds : bond 0.03066 ( 128) hydrogen bonds : angle 3.89874 ( 372) *********************** 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 83 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.187 Fit side-chains REVERT: A 10 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7747 (ttm-80) REVERT: A 30 ARG cc_start: 0.6802 (tmt170) cc_final: 0.6481 (tmt170) REVERT: A 381 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6648 (ttt90) REVERT: B 22 MET cc_start: 0.7549 (ttm) cc_final: 0.7345 (ttm) REVERT: B 30 ARG cc_start: 0.6916 (tmt170) cc_final: 0.6631 (tmt170) REVERT: B 345 GLN cc_start: 0.8113 (mt0) cc_final: 0.7829 (mt0) REVERT: B 359 GLU cc_start: 0.7611 (mp0) cc_final: 0.7037 (mt-10) REVERT: B 388 ILE cc_start: 0.7788 (mt) cc_final: 0.7392 (pt) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.0660 time to fit residues: 7.0866 Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 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 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 68 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 = 0.4258 r_free = 0.4258 target = 0.190489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131895 restraints weight = 5520.784| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.84 r_work: 0.3426 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5174 Z= 0.104 Angle : 0.606 18.064 7038 Z= 0.284 Chirality : 0.041 0.132 838 Planarity : 0.003 0.030 878 Dihedral : 5.401 22.172 686 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.45 % Allowed : 14.67 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.33), residues: 642 helix: -2.17 (0.27), residues: 352 sheet: 0.45 (0.85), residues: 46 loop : -2.25 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.014 0.001 TYR B 270 PHE 0.009 0.001 PHE A 94 TRP 0.009 0.001 TRP A 375 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5172) covalent geometry : angle 0.60599 ( 7034) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.43122 ( 4) hydrogen bonds : bond 0.02627 ( 128) hydrogen bonds : angle 3.76192 ( 372) *********************** 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 70 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7825 (ttm-80) REVERT: A 30 ARG cc_start: 0.6768 (tmt170) cc_final: 0.6490 (tmt170) REVERT: B 22 MET cc_start: 0.7520 (ttm) cc_final: 0.7318 (ttm) REVERT: B 30 ARG cc_start: 0.6877 (tmt170) cc_final: 0.6621 (tmt170) REVERT: B 388 ILE cc_start: 0.7825 (mt) cc_final: 0.7453 (pt) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.0747 time to fit residues: 6.8629 Evaluate side-chains 66 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 68 GLN 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 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 7 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 68 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 = 0.4306 r_free = 0.4306 target = 0.196091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137717 restraints weight = 5450.238| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.84 r_work: 0.3497 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5174 Z= 0.081 Angle : 0.590 17.106 7038 Z= 0.275 Chirality : 0.040 0.132 838 Planarity : 0.003 0.029 878 Dihedral : 4.924 21.306 686 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.91 % Allowed : 15.22 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.33), residues: 642 helix: -1.84 (0.27), residues: 364 sheet: 0.72 (0.84), residues: 46 loop : -2.66 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.010 0.001 TYR B 270 PHE 0.006 0.001 PHE B 21 TRP 0.008 0.001 TRP A 375 HIS 0.001 0.000 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 5172) covalent geometry : angle 0.59044 ( 7034) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.51012 ( 4) hydrogen bonds : bond 0.02000 ( 128) hydrogen bonds : angle 3.48543 ( 372) ********************** 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 64 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7744 (ttm-80) REVERT: B 65 HIS cc_start: 0.8142 (m-70) cc_final: 0.7659 (t-90) REVERT: B 245 MET cc_start: 0.8259 (mmm) cc_final: 0.7976 (mmm) REVERT: B 388 ILE cc_start: 0.7675 (mt) cc_final: 0.7463 (pt) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 0.0559 time to fit residues: 4.9188 Evaluate side-chains 65 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 GLN 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: 0.9980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 68 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 = 0.4294 r_free = 0.4294 target = 0.194745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138957 restraints weight = 5480.364| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.57 r_work: 0.3485 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5174 Z= 0.087 Angle : 0.595 16.795 7038 Z= 0.274 Chirality : 0.041 0.132 838 Planarity : 0.003 0.030 878 Dihedral : 4.915 20.808 686 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.27 % Allowed : 14.86 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.33), residues: 642 helix: -1.75 (0.28), residues: 362 sheet: 0.98 (0.86), residues: 46 loop : -2.56 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.013 0.001 TYR B 270 PHE 0.007 0.001 PHE A 94 TRP 0.008 0.001 TRP B 375 HIS 0.001 0.000 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 5172) covalent geometry : angle 0.59474 ( 7034) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.49020 ( 4) hydrogen bonds : bond 0.02173 ( 128) hydrogen bonds : angle 3.39595 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1297.93 seconds wall clock time: 22 minutes 48.98 seconds (1368.98 seconds total)