Starting phenix.real_space_refine on Sat May 17 15:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymr_39405/05_2025/8ymr_39405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymr_39405/05_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_39405/05_2025/8ymr_39405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymr_39405/05_2025/8ymr_39405.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymr_39405/05_2025/8ymr_39405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymr_39405/05_2025/8ymr_39405.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.07, per 1000 atoms: 0.50 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: 3.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.26 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: 5.46 Time building geometry restraints manager: 4.55 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: 0.03 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: 1.030 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: 0.300 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 34.440 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP B 145 HIS 0.005 0.001 HIS A 233 PHE 0.016 0.001 PHE A 321 TYR 0.007 0.001 TYR A 199 ARG 0.011 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.12504 ( 439) hydrogen bonds : angle 5.81498 ( 1320) SS BOND : bond 0.00366 ( 12) SS BOND : angle 0.99027 ( 24) covalent geometry : bond 0.00271 ( 9018) covalent geometry : angle 0.56902 (12252) *********************** 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 : 1.322 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: 0.5872 (mmm) REVERT: C 118 ASP cc_start: 0.7270 (m-30) cc_final: 0.6902 (t0) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.3679 time to fit residues: 68.2696 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 : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.146175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113964 restraints weight = 27582.671| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.24 r_work: 0.3056 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9030 Z= 0.169 Angle : 0.596 15.837 12276 Z= 0.327 Chirality : 0.044 0.154 1365 Planarity : 0.005 0.064 1581 Dihedral : 4.642 32.293 1206 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.85 % Favored : 92.59 % Rotamer: Outliers : 1.12 % Allowed : 4.28 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1080 helix: 0.84 (0.26), residues: 402 sheet: -2.22 (0.30), residues: 282 loop : -2.13 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 145 HIS 0.006 0.002 HIS B 231 PHE 0.016 0.001 PHE A 321 TYR 0.008 0.001 TYR A 199 ARG 0.006 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 439) hydrogen bonds : angle 4.72011 ( 1320) SS BOND : bond 0.00602 ( 12) SS BOND : angle 2.18511 ( 24) covalent geometry : bond 0.00390 ( 9018) covalent geometry : angle 0.58839 (12252) *********************** 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 115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8763 (pt0) cc_final: 0.8528 (pt0) REVERT: A 119 MET cc_start: 0.8348 (tmm) cc_final: 0.8040 (tmm) REVERT: B 284 GLU cc_start: 0.7378 (tt0) cc_final: 0.7177 (tp30) REVERT: C 118 ASP cc_start: 0.7821 (m-30) cc_final: 0.7025 (t0) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.3854 time to fit residues: 62.0514 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118223 restraints weight = 27234.552| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.20 r_work: 0.3241 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9030 Z= 0.115 Angle : 0.543 15.806 12276 Z= 0.299 Chirality : 0.043 0.151 1365 Planarity : 0.004 0.058 1581 Dihedral : 4.441 25.866 1206 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.02 % Allowed : 6.93 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1080 helix: 1.41 (0.27), residues: 384 sheet: -2.35 (0.29), residues: 294 loop : -1.86 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.004 0.001 HIS B 231 PHE 0.012 0.001 PHE A 321 TYR 0.008 0.001 TYR A 199 ARG 0.006 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 439) hydrogen bonds : angle 4.37275 ( 1320) SS BOND : bond 0.00319 ( 12) SS BOND : angle 1.50283 ( 24) covalent geometry : bond 0.00259 ( 9018) covalent geometry : angle 0.53912 (12252) *********************** 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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 ASP cc_start: 0.7819 (m-30) cc_final: 0.7029 (t0) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.3435 time to fit residues: 63.4928 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 402 ILE Chi-restraints excluded: chain B residue 135 ASP 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 28 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.144587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112324 restraints weight = 27511.822| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.24 r_work: 0.3068 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9030 Z= 0.144 Angle : 0.556 15.819 12276 Z= 0.306 Chirality : 0.044 0.212 1365 Planarity : 0.005 0.065 1581 Dihedral : 4.467 25.631 1206 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 7.44 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1080 helix: 1.20 (0.27), residues: 402 sheet: -2.00 (0.31), residues: 276 loop : -2.00 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 145 HIS 0.005 0.001 HIS B 231 PHE 0.014 0.001 PHE C 321 TYR 0.008 0.001 TYR A 199 ARG 0.008 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02646 ( 439) hydrogen bonds : angle 4.29908 ( 1320) SS BOND : bond 0.00630 ( 12) SS BOND : angle 1.62976 ( 24) covalent geometry : bond 0.00332 ( 9018) covalent geometry : angle 0.55163 (12252) *********************** 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: 19 poor density : 111 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6590 (p90) REVERT: C 118 ASP cc_start: 0.7860 (m-30) cc_final: 0.7059 (t0) outliers start: 19 outliers final: 11 residues processed: 124 average time/residue: 0.3528 time to fit residues: 63.1972 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 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 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 275 ASP 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 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 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 = 0.3650 r_free = 0.3650 target = 0.145995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115499 restraints weight = 27715.191| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.13 r_work: 0.3074 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9030 Z= 0.129 Angle : 0.543 15.821 12276 Z= 0.298 Chirality : 0.043 0.149 1365 Planarity : 0.005 0.068 1581 Dihedral : 4.424 25.161 1206 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.63 % Allowed : 8.26 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1080 helix: 1.54 (0.28), residues: 384 sheet: -1.97 (0.31), residues: 276 loop : -1.95 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.005 0.001 HIS B 231 PHE 0.014 0.001 PHE B 321 TYR 0.008 0.001 TYR A 199 ARG 0.007 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 439) hydrogen bonds : angle 4.20921 ( 1320) SS BOND : bond 0.00399 ( 12) SS BOND : angle 1.66074 ( 24) covalent geometry : bond 0.00298 ( 9018) covalent geometry : angle 0.53843 (12252) *********************** 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 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6723 (p90) REVERT: A 406 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6333 (mp) REVERT: B 397 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6171 (p90) REVERT: C 118 ASP cc_start: 0.7867 (m-30) cc_final: 0.7038 (t0) outliers start: 16 outliers final: 9 residues processed: 121 average time/residue: 0.3411 time to fit residues: 60.9680 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 397 PHE 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 135 ASP Chi-restraints excluded: chain C residue 166 ILE 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 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.110736 restraints weight = 27633.692| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.11 r_work: 0.3008 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9030 Z= 0.222 Angle : 0.602 15.781 12276 Z= 0.330 Chirality : 0.045 0.173 1365 Planarity : 0.005 0.065 1581 Dihedral : 4.681 25.703 1206 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 8.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1080 helix: 1.25 (0.27), residues: 390 sheet: -2.06 (0.30), residues: 276 loop : -1.86 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 145 HIS 0.008 0.002 HIS B 231 PHE 0.021 0.002 PHE B 321 TYR 0.009 0.001 TYR A 199 ARG 0.008 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 439) hydrogen bonds : angle 4.42504 ( 1320) SS BOND : bond 0.00603 ( 12) SS BOND : angle 2.04171 ( 24) covalent geometry : bond 0.00522 ( 9018) covalent geometry : angle 0.59540 (12252) *********************** 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 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.6875 (p90) REVERT: A 406 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6335 (mt) REVERT: B 397 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6428 (p90) REVERT: C 118 ASP cc_start: 0.7899 (m-30) cc_final: 0.7089 (t0) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.3544 time to fit residues: 58.3515 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 269 THR 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 7 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107203 restraints weight = 27848.435| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.25 r_work: 0.3000 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9030 Z= 0.190 Angle : 0.582 15.770 12276 Z= 0.319 Chirality : 0.045 0.149 1365 Planarity : 0.005 0.086 1581 Dihedral : 4.714 25.451 1206 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.30 % Favored : 93.15 % Rotamer: Outliers : 1.94 % Allowed : 9.89 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1080 helix: 1.32 (0.27), residues: 387 sheet: -2.15 (0.30), residues: 282 loop : -1.89 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.005 0.002 HIS B 231 PHE 0.016 0.002 PHE A 321 TYR 0.009 0.001 TYR A 199 ARG 0.009 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02745 ( 439) hydrogen bonds : angle 4.38507 ( 1320) SS BOND : bond 0.00529 ( 12) SS BOND : angle 1.87119 ( 24) covalent geometry : bond 0.00443 ( 9018) covalent geometry : angle 0.57633 (12252) *********************** 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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7135 (p90) REVERT: A 406 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6408 (mt) REVERT: B 397 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6379 (p90) REVERT: C 118 ASP cc_start: 0.7896 (m-30) cc_final: 0.7062 (t0) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.3468 time to fit residues: 58.2345 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 166 ILE Chi-restraints excluded: chain C residue 341 CYS 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 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 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 = 0.3634 r_free = 0.3634 target = 0.144574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114311 restraints weight = 27258.481| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.09 r_work: 0.3052 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1829 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= 0.133 Angle : 0.553 15.806 12276 Z= 0.302 Chirality : 0.043 0.147 1365 Planarity : 0.005 0.098 1581 Dihedral : 4.583 24.853 1206 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.85 % Favored : 92.59 % Rotamer: Outliers : 1.83 % Allowed : 10.50 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 1080 helix: 1.47 (0.27), residues: 387 sheet: -2.42 (0.29), residues: 300 loop : -1.61 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS B 231 PHE 0.011 0.001 PHE A 321 TYR 0.009 0.001 TYR A 199 ARG 0.009 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02550 ( 439) hydrogen bonds : angle 4.23741 ( 1320) SS BOND : bond 0.00423 ( 12) SS BOND : angle 1.75080 ( 24) covalent geometry : bond 0.00306 ( 9018) covalent geometry : angle 0.54802 (12252) *********************** 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 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7172 (p90) REVERT: A 406 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6376 (mp) REVERT: B 397 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6309 (p90) REVERT: C 118 ASP cc_start: 0.7860 (m-30) cc_final: 0.6996 (t0) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.3452 time to fit residues: 61.0701 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.147752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116100 restraints weight = 27325.649| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.19 r_work: 0.3092 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9030 Z= 0.105 Angle : 0.538 15.847 12276 Z= 0.293 Chirality : 0.043 0.147 1365 Planarity : 0.004 0.077 1581 Dihedral : 4.405 23.537 1206 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.20 % Favored : 93.24 % Rotamer: Outliers : 1.73 % Allowed : 11.01 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1080 helix: 1.64 (0.27), residues: 387 sheet: -2.27 (0.30), residues: 294 loop : -1.60 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.003 0.001 HIS C 231 PHE 0.008 0.001 PHE A 321 TYR 0.008 0.001 TYR A 199 ARG 0.008 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02374 ( 439) hydrogen bonds : angle 4.07802 ( 1320) SS BOND : bond 0.00369 ( 12) SS BOND : angle 1.78957 ( 24) covalent geometry : bond 0.00243 ( 9018) covalent geometry : angle 0.53239 (12252) *********************** 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: 17 poor density : 113 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7183 (p90) REVERT: B 118 ASP cc_start: 0.7677 (m-30) cc_final: 0.6876 (t0) REVERT: B 397 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6191 (p90) REVERT: C 118 ASP cc_start: 0.7851 (m-30) cc_final: 0.6970 (t0) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.3509 time to fit residues: 61.1803 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 177 GLN 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 76 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.146364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116260 restraints weight = 27444.004| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3134 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9030 Z= 0.120 Angle : 0.552 15.841 12276 Z= 0.301 Chirality : 0.043 0.160 1365 Planarity : 0.005 0.094 1581 Dihedral : 4.504 26.876 1206 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.73 % Allowed : 10.91 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1080 helix: 1.64 (0.27), residues: 387 sheet: -2.23 (0.30), residues: 294 loop : -1.55 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.004 0.001 HIS C 231 PHE 0.010 0.001 PHE A 321 TYR 0.008 0.001 TYR A 199 ARG 0.009 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02449 ( 439) hydrogen bonds : angle 4.09647 ( 1320) SS BOND : bond 0.00594 ( 12) SS BOND : angle 2.04821 ( 24) covalent geometry : bond 0.00282 ( 9018) covalent geometry : angle 0.54542 (12252) ********************** 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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7347 (p90) REVERT: A 406 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6421 (mp) REVERT: B 118 ASP cc_start: 0.7707 (m-30) cc_final: 0.6922 (t0) REVERT: B 397 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6297 (p90) REVERT: C 118 ASP cc_start: 0.7851 (m-30) cc_final: 0.6990 (t0) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.3335 time to fit residues: 58.0117 Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 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 177 GLN 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 83 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.143026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111062 restraints weight = 27566.435| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.22 r_work: 0.3015 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9030 Z= 0.166 Angle : 0.574 15.810 12276 Z= 0.313 Chirality : 0.044 0.148 1365 Planarity : 0.005 0.087 1581 Dihedral : 4.671 29.225 1206 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.48 % Favored : 92.96 % Rotamer: Outliers : 1.63 % Allowed : 11.42 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1080 helix: 1.25 (0.27), residues: 408 sheet: -1.93 (0.31), residues: 276 loop : -1.78 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.006 0.002 HIS C 231 PHE 0.015 0.001 PHE A 321 TYR 0.010 0.001 TYR C 265 ARG 0.010 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02636 ( 439) hydrogen bonds : angle 4.20209 ( 1320) SS BOND : bond 0.00460 ( 12) SS BOND : angle 2.16209 ( 24) covalent geometry : bond 0.00391 ( 9018) covalent geometry : angle 0.56682 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7819.89 seconds wall clock time: 134 minutes 49.83 seconds (8089.83 seconds total)