Starting phenix.real_space_refine on Sun Aug 24 00:58:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymr_39405/08_2025/8ymr_39405.cif" } resolution = 3.09 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= 0.000 sd= 0.036 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5652 2.51 5 N 1482 2.21 5 O 1611 1.98 5 H 7239 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16041 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5347 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5347 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "C" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5347 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Time building chain proxies: 3.51, per 1000 atoms: 0.22 Number of scatterers: 16041 At special positions: 0 Unit cell: (94.86, 100.44, 123.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1611 8.00 N 1482 7.00 C 5652 6.00 H 7239 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS C 311 " 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: 1.39 Conformation dependent library (CDL) restraints added in 522.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 39.7% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 53 through 84 removed outlier: 4.080A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.802A pdb=" N MET A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.871A pdb=" N SER A 237 " --> pdb=" O HIS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.791A pdb=" N ALA A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.584A pdb=" N GLN A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.792A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.669A pdb=" N GLU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 84 Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 113 through 124 removed outlier: 4.122A pdb=" N MET B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.601A pdb=" N SER B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 275 through 296 removed outlier: 3.692A pdb=" N ALA B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.566A pdb=" N GLN B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.871A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.581A pdb=" N VAL B 405 " --> pdb=" O CYS B 401 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 83 Processing helix chain 'C' and resid 109 through 112 Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.869A pdb=" N MET C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.513A pdb=" N LEU C 133 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.518A pdb=" N SER C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 275 through 296 removed outlier: 3.730A pdb=" N ALA C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.695A pdb=" N GLN C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 397 removed outlier: 3.933A pdb=" N PHE C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.713A pdb=" N GLU C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 7.779A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 256 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 7.779A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 7.480A pdb=" N GLN A 187 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94 removed outlier: 7.882A pdb=" N TYR B 371 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 260 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94 removed outlier: 7.882A pdb=" N TYR B 371 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 260 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 255 " --> pdb=" O MET B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 removed outlier: 7.220A pdb=" N GLN B 187 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94 removed outlier: 7.873A pdb=" N TYR C 371 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE C 260 " --> pdb=" O TYR C 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94 removed outlier: 7.873A pdb=" N TYR C 371 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE C 260 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 255 " --> pdb=" O MET C 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 183 removed outlier: 7.377A pdb=" N GLN C 187 " --> pdb=" O PRO C 107 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7236 1.03 - 1.23: 103 1.23 - 1.43: 3797 1.43 - 1.62: 5040 1.62 - 1.82: 81 Bond restraints: 16257 Sorted by residual: bond pdb=" CG GLN C 73 " pdb=" CD GLN C 73 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 8.95e-01 bond pdb=" CG GLN B 73 " pdb=" CD GLN B 73 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.65e-01 bond pdb=" CG GLN A 73 " pdb=" CD GLN A 73 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 6.73e-01 bond pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.53e-01 bond pdb=" CB ILE A 189 " pdb=" CG2 ILE A 189 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.40e-01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.38: 28656 10.38 - 20.77: 3 20.77 - 31.15: 18 31.15 - 41.53: 0 41.53 - 51.92: 6 Bond angle restraints: 28683 Sorted by residual: angle pdb=" C THR A 114 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 124.72 72.80 51.92 3.00e+00 1.11e-01 2.99e+02 angle pdb=" CA ILE A 115 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 114.42 62.52 51.90 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C THR B 114 " pdb=" N ILE B 115 " pdb=" H ILE B 115 " ideal model delta sigma weight residual 124.72 72.86 51.86 3.00e+00 1.11e-01 2.99e+02 angle pdb=" CA ILE C 115 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 114.42 62.60 51.82 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C THR C 114 " pdb=" N ILE C 115 " pdb=" H ILE C 115 " ideal model delta sigma weight residual 124.72 72.92 51.80 3.00e+00 1.11e-01 2.98e+02 ... (remaining 28678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 7134 17.58 - 35.15: 573 35.15 - 52.73: 133 52.73 - 70.31: 27 70.31 - 87.88: 11 Dihedral angle restraints: 7878 sinusoidal: 4134 harmonic: 3744 Sorted by residual: dihedral pdb=" CB CYS B 273 " pdb=" SG CYS B 273 " pdb=" SG CYS B 341 " pdb=" CB CYS B 341 " ideal model delta sinusoidal sigma weight residual 93.00 39.46 53.54 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA CYS C 106 " pdb=" C CYS C 106 " pdb=" N PRO C 107 " pdb=" CA PRO C 107 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 946 0.037 - 0.073: 275 0.073 - 0.110: 92 0.110 - 0.147: 49 0.147 - 0.183: 3 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA GLN C 73 " pdb=" N GLN C 73 " pdb=" C GLN C 73 " pdb=" CB GLN C 73 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA GLN B 73 " pdb=" N GLN B 73 " pdb=" C GLN B 73 " pdb=" CB GLN B 73 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA GLN A 73 " pdb=" N GLN A 73 " pdb=" C GLN A 73 " pdb=" CB GLN A 73 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 1362 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 84 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 85 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 84 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 85 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 136 " -0.185 9.50e-02 1.11e+02 6.21e-02 4.66e+00 pdb=" NE ARG A 136 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 136 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 136 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 136 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 136 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 136 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 136 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 136 " -0.000 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 248 2.09 - 2.72: 25368 2.72 - 3.35: 44673 3.35 - 3.97: 58960 3.97 - 4.60: 91233 Nonbonded interactions: 220482 Sorted by model distance: nonbonded pdb=" O ASN A 174 " pdb="HD21 ASN A 174 " model vdw 1.469 2.450 nonbonded pdb="HH22 ARG B 238 " pdb=" OE2 GLU B 284 " model vdw 1.570 2.450 nonbonded pdb=" H ILE C 115 " pdb=" HA ILE C 115 " model vdw 1.593 1.816 nonbonded pdb=" H ILE A 115 " pdb=" HA ILE A 115 " model vdw 1.594 1.816 nonbonded pdb=" H ILE B 115 " pdb=" HA ILE B 115 " model vdw 1.597 1.816 ... (remaining 220477 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' selection = chain 'C' } 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: 1.090 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.003 0.030 9030 Z= 0.127 Angle : 0.570 14.660 12276 Z= 0.333 Chirality : 0.044 0.183 1365 Planarity : 0.005 0.081 1581 Dihedral : 13.581 87.884 3306 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.83 % Favored : 93.61 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % 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: -1.67 (0.26), residues: 1080 helix: 0.78 (0.27), residues: 396 sheet: -2.26 (0.30), residues: 279 loop : -2.06 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 136 TYR 0.007 0.001 TYR A 199 PHE 0.016 0.001 PHE A 321 TRP 0.006 0.001 TRP B 145 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9018) covalent geometry : angle 0.56902 (12252) SS BOND : bond 0.00366 ( 12) SS BOND : angle 0.99027 ( 24) hydrogen bonds : bond 0.12504 ( 439) hydrogen bonds : angle 5.81498 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.6615 (mmm) cc_final: 0.5873 (mmm) REVERT: C 118 ASP cc_start: 0.7270 (m-30) cc_final: 0.6899 (t0) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1767 time to fit residues: 33.0739 Evaluate side-chains 97 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116276 restraints weight = 27413.764| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.15 r_work: 0.3064 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9030 Z= 0.163 Angle : 0.595 15.829 12276 Z= 0.327 Chirality : 0.044 0.153 1365 Planarity : 0.005 0.069 1581 Dihedral : 4.653 33.808 1206 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Rotamer: Outliers : 1.02 % Allowed : 4.69 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.62 (0.25), residues: 1080 helix: 0.84 (0.26), residues: 402 sheet: -2.22 (0.30), residues: 282 loop : -2.12 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 136 TYR 0.008 0.001 TYR A 199 PHE 0.016 0.001 PHE A 321 TRP 0.009 0.001 TRP B 145 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9018) covalent geometry : angle 0.58923 (12252) SS BOND : bond 0.00789 ( 12) SS BOND : angle 1.97609 ( 24) hydrogen bonds : bond 0.03103 ( 439) hydrogen bonds : angle 4.68892 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8699 (pt0) cc_final: 0.8472 (pt0) REVERT: A 119 MET cc_start: 0.8331 (tmm) cc_final: 0.8006 (tmm) REVERT: C 118 ASP cc_start: 0.7818 (m-30) cc_final: 0.7014 (t0) REVERT: C 363 MET cc_start: 0.7977 (ttt) cc_final: 0.7747 (tpp) outliers start: 10 outliers final: 7 residues processed: 111 average time/residue: 0.1640 time to fit residues: 25.9052 Evaluate side-chains 104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.113246 restraints weight = 27708.412| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.13 r_work: 0.3050 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9030 Z= 0.163 Angle : 0.568 15.817 12276 Z= 0.313 Chirality : 0.044 0.154 1365 Planarity : 0.005 0.058 1581 Dihedral : 4.566 26.182 1206 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Rotamer: Outliers : 1.22 % Allowed : 7.44 % Favored : 91.34 % 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: -1.36 (0.25), residues: 1080 helix: 1.30 (0.27), residues: 384 sheet: -2.10 (0.30), residues: 276 loop : -2.11 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.016 0.001 PHE C 321 TRP 0.008 0.001 TRP C 145 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9018) covalent geometry : angle 0.56376 (12252) SS BOND : bond 0.00404 ( 12) SS BOND : angle 1.68773 ( 24) hydrogen bonds : bond 0.02883 ( 439) hydrogen bonds : angle 4.48814 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8672 (pt0) cc_final: 0.8446 (pt0) REVERT: A 119 MET cc_start: 0.8359 (tmm) cc_final: 0.8145 (tmm) REVERT: C 118 ASP cc_start: 0.7865 (m-30) cc_final: 0.7066 (t0) REVERT: C 288 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7052 (mp0) outliers start: 12 outliers final: 5 residues processed: 118 average time/residue: 0.1687 time to fit residues: 29.1254 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.144583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114120 restraints weight = 27384.751| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.10 r_work: 0.3048 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9030 Z= 0.178 Angle : 0.575 15.811 12276 Z= 0.317 Chirality : 0.045 0.215 1365 Planarity : 0.005 0.063 1581 Dihedral : 4.626 26.166 1206 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Rotamer: Outliers : 2.04 % Allowed : 8.05 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.25), residues: 1080 helix: 1.33 (0.27), residues: 384 sheet: -2.09 (0.30), residues: 276 loop : -2.04 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.017 0.001 PHE B 321 TRP 0.007 0.001 TRP C 145 HIS 0.006 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9018) covalent geometry : angle 0.57077 (12252) SS BOND : bond 0.00550 ( 12) SS BOND : angle 1.73163 ( 24) hydrogen bonds : bond 0.02784 ( 439) hydrogen bonds : angle 4.42848 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.8941 (m-80) cc_final: 0.8739 (m-80) REVERT: A 397 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.6653 (p90) REVERT: A 406 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6389 (mp) REVERT: C 118 ASP cc_start: 0.7852 (m-30) cc_final: 0.7059 (t0) REVERT: C 288 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7009 (mp0) outliers start: 20 outliers final: 10 residues processed: 123 average time/residue: 0.1656 time to fit residues: 30.1814 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111598 restraints weight = 27542.275| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.24 r_work: 0.3049 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9030 Z= 0.164 Angle : 0.567 15.807 12276 Z= 0.311 Chirality : 0.044 0.154 1365 Planarity : 0.005 0.066 1581 Dihedral : 4.606 25.787 1206 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.73 % Allowed : 9.17 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.26), residues: 1080 helix: 1.01 (0.27), residues: 408 sheet: -2.11 (0.30), residues: 276 loop : -1.94 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.017 0.001 PHE B 321 TRP 0.008 0.001 TRP C 145 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9018) covalent geometry : angle 0.56144 (12252) SS BOND : bond 0.00426 ( 12) SS BOND : angle 1.89353 ( 24) hydrogen bonds : bond 0.02703 ( 439) hydrogen bonds : angle 4.35905 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.6885 (p90) REVERT: B 397 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6434 (p90) REVERT: C 118 ASP cc_start: 0.7888 (m-30) cc_final: 0.7073 (t0) REVERT: C 288 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6987 (mp0) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.1613 time to fit residues: 27.1886 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110692 restraints weight = 27423.879| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.11 r_work: 0.3007 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9030 Z= 0.201 Angle : 0.589 15.820 12276 Z= 0.323 Chirality : 0.045 0.169 1365 Planarity : 0.005 0.067 1581 Dihedral : 4.694 25.500 1206 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 10.30 % Favored : 87.77 % 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: -1.28 (0.26), residues: 1080 helix: 1.24 (0.27), residues: 390 sheet: -2.17 (0.30), residues: 282 loop : -1.85 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 136 TYR 0.011 0.001 TYR C 239 PHE 0.017 0.002 PHE B 321 TRP 0.007 0.001 TRP C 145 HIS 0.007 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 9018) covalent geometry : angle 0.58341 (12252) SS BOND : bond 0.00592 ( 12) SS BOND : angle 1.86159 ( 24) hydrogen bonds : bond 0.02793 ( 439) hydrogen bonds : angle 4.42383 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6926 (p90) REVERT: A 406 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6269 (mt) REVERT: B 397 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6471 (p90) REVERT: C 118 ASP cc_start: 0.7870 (m-30) cc_final: 0.7086 (t0) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.1626 time to fit residues: 27.4144 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115209 restraints weight = 27254.254| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.09 r_work: 0.3063 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9030 Z= 0.114 Angle : 0.540 15.849 12276 Z= 0.296 Chirality : 0.043 0.150 1365 Planarity : 0.005 0.105 1581 Dihedral : 4.538 24.642 1206 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.63 % Allowed : 11.21 % Favored : 87.16 % 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: -1.08 (0.26), residues: 1080 helix: 1.58 (0.27), residues: 384 sheet: -2.36 (0.29), residues: 294 loop : -1.58 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.010 0.001 PHE A 321 TRP 0.008 0.001 TRP C 145 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9018) covalent geometry : angle 0.53619 (12252) SS BOND : bond 0.00487 ( 12) SS BOND : angle 1.54869 ( 24) hydrogen bonds : bond 0.02476 ( 439) hydrogen bonds : angle 4.22068 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7048 (p90) REVERT: A 406 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6326 (mp) REVERT: B 397 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6308 (p90) REVERT: C 118 ASP cc_start: 0.7872 (m-30) cc_final: 0.7069 (t0) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.1710 time to fit residues: 29.4138 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.141633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111165 restraints weight = 27778.368| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.12 r_work: 0.3020 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9030 Z= 0.178 Angle : 0.577 15.835 12276 Z= 0.315 Chirality : 0.044 0.152 1365 Planarity : 0.005 0.088 1581 Dihedral : 4.707 26.645 1206 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.48 % Favored : 92.96 % Rotamer: Outliers : 2.14 % Allowed : 10.70 % Favored : 87.16 % 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: -1.22 (0.26), residues: 1080 helix: 1.30 (0.27), residues: 390 sheet: -2.17 (0.30), residues: 276 loop : -1.83 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.014 0.001 PHE A 321 TRP 0.006 0.001 TRP C 145 HIS 0.006 0.002 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9018) covalent geometry : angle 0.57011 (12252) SS BOND : bond 0.00441 ( 12) SS BOND : angle 2.03462 ( 24) hydrogen bonds : bond 0.02729 ( 439) hydrogen bonds : angle 4.33030 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7088 (p90) REVERT: A 406 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6425 (mt) REVERT: B 397 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6370 (p90) REVERT: C 118 ASP cc_start: 0.7868 (m-30) cc_final: 0.7075 (t0) outliers start: 21 outliers final: 14 residues processed: 116 average time/residue: 0.1445 time to fit residues: 24.5731 Evaluate side-chains 120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114948 restraints weight = 27292.130| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.11 r_work: 0.3061 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9030 Z= 0.130 Angle : 0.552 15.830 12276 Z= 0.303 Chirality : 0.043 0.156 1365 Planarity : 0.005 0.090 1581 Dihedral : 4.642 28.878 1206 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 11.01 % Favored : 87.05 % 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: -1.21 (0.26), residues: 1080 helix: 1.22 (0.27), residues: 408 sheet: -2.45 (0.29), residues: 294 loop : -1.51 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.009 0.001 TYR A 199 PHE 0.010 0.001 PHE A 321 TRP 0.007 0.001 TRP A 145 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9018) covalent geometry : angle 0.54618 (12252) SS BOND : bond 0.00499 ( 12) SS BOND : angle 1.92409 ( 24) hydrogen bonds : bond 0.02532 ( 439) hydrogen bonds : angle 4.18270 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7153 (p90) REVERT: A 406 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6371 (mp) REVERT: B 118 ASP cc_start: 0.7693 (m-30) cc_final: 0.6917 (t0) REVERT: B 397 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.6376 (p90) REVERT: C 118 ASP cc_start: 0.7842 (m-30) cc_final: 0.6998 (t0) outliers start: 19 outliers final: 12 residues processed: 121 average time/residue: 0.1541 time to fit residues: 26.5603 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107212 restraints weight = 27669.198| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.22 r_work: 0.3105 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9030 Z= 0.102 Angle : 0.533 15.846 12276 Z= 0.290 Chirality : 0.043 0.147 1365 Planarity : 0.005 0.088 1581 Dihedral : 4.487 30.529 1206 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Rotamer: Outliers : 1.53 % Allowed : 11.42 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.95 (0.26), residues: 1080 helix: 1.41 (0.27), residues: 408 sheet: -1.94 (0.31), residues: 276 loop : -1.75 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.008 0.001 TYR A 199 PHE 0.008 0.001 PHE A 321 TRP 0.008 0.001 TRP A 145 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9018) covalent geometry : angle 0.52871 (12252) SS BOND : bond 0.00392 ( 12) SS BOND : angle 1.58010 ( 24) hydrogen bonds : bond 0.02338 ( 439) hydrogen bonds : angle 4.03227 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7208 (p90) REVERT: A 406 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6402 (mp) REVERT: B 118 ASP cc_start: 0.7687 (m-30) cc_final: 0.6920 (t0) REVERT: B 397 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6383 (p90) REVERT: C 118 ASP cc_start: 0.7839 (m-30) cc_final: 0.7003 (t0) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.1635 time to fit residues: 28.3756 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113142 restraints weight = 27368.141| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.13 r_work: 0.3038 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9030 Z= 0.192 Angle : 0.588 15.835 12276 Z= 0.322 Chirality : 0.045 0.164 1365 Planarity : 0.006 0.107 1581 Dihedral : 4.765 30.580 1206 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.30 % Favored : 93.15 % Rotamer: Outliers : 1.43 % Allowed : 11.93 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.17 (0.26), residues: 1080 helix: 1.19 (0.27), residues: 408 sheet: -2.05 (0.30), residues: 282 loop : -1.81 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 136 TYR 0.009 0.001 TYR A 199 PHE 0.015 0.002 PHE A 321 TRP 0.006 0.001 TRP C 145 HIS 0.006 0.002 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9018) covalent geometry : angle 0.58026 (12252) SS BOND : bond 0.00439 ( 12) SS BOND : angle 2.27018 ( 24) hydrogen bonds : bond 0.02685 ( 439) hydrogen bonds : angle 4.22166 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.79 seconds wall clock time: 64 minutes 46.90 seconds (3886.90 seconds total)