Starting phenix.real_space_refine on Sat Jun 14 06:19:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymr_39405/06_2025/8ymr_39405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymr_39405/06_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_39405/06_2025/8ymr_39405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymr_39405/06_2025/8ymr_39405.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymr_39405/06_2025/8ymr_39405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymr_39405/06_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-5710/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: 8.26, per 1000 atoms: 0.51 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: 4.50 Conformation dependent library (CDL) restraints added in 1.5 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: 1.55 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: 5.43 Time building geometry restraints manager: 5.20 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: 0.920 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.680 Find NCS groups from input model: 0.500 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- 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 : 1.331 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: 0.3782 time to fit residues: 70.2842 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 : 1.396 ------------------------------------------------------------------------------- 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 = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113966 restraints weight = 27583.457| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.24 r_work: 0.3055 rms_B_bonded: 2.47 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: 0.7730 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 : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8759 (pt0) cc_final: 0.8526 (pt0) REVERT: A 119 MET cc_start: 0.8346 (tmm) cc_final: 0.8038 (tmm) REVERT: B 284 GLU cc_start: 0.7376 (tt0) cc_final: 0.7175 (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: 0.3749 time to fit residues: 60.0368 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 : 1.260 ------------------------------------------------------------------------------- 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: 0.4980 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 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: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.147116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116504 restraints weight = 27179.755| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.15 r_work: 0.3068 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1127 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= 0.130 Angle : 0.550 15.800 12276 Z= 0.303 Chirality : 0.043 0.152 1365 Planarity : 0.005 0.058 1581 Dihedral : 4.489 26.286 1206 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.57 % Favored : 92.87 % Rotamer: Outliers : 1.02 % Allowed : 6.83 % Favored : 92.15 % 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: -1.39 (0.25), residues: 1080 helix: 1.10 (0.27), residues: 402 sheet: -2.06 (0.30), residues: 276 loop : -2.11 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.005 0.001 HIS B 231 PHE 0.014 0.001 PHE A 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 0.02765 ( 439) hydrogen bonds : angle 4.40928 ( 1320) SS BOND : bond 0.00355 ( 12) SS BOND : angle 1.56454 ( 24) covalent geometry : bond 0.00297 ( 9018) covalent geometry : angle 0.54624 (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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8664 (pt0) cc_final: 0.8406 (pt0) REVERT: B 284 GLU cc_start: 0.7365 (tt0) cc_final: 0.7125 (tp30) REVERT: C 118 ASP cc_start: 0.7851 (m-30) cc_final: 0.7035 (t0) REVERT: C 239 TYR cc_start: 0.8779 (m-80) cc_final: 0.8567 (m-80) outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.3661 time to fit residues: 64.7977 Evaluate side-chains 110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.146984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116623 restraints weight = 27234.088| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.12 r_work: 0.3136 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9030 Z= 0.134 Angle : 0.552 15.821 12276 Z= 0.304 Chirality : 0.044 0.217 1365 Planarity : 0.004 0.065 1581 Dihedral : 4.472 25.855 1206 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.83 % Allowed : 7.44 % Favored : 90.72 % 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: -1.24 (0.26), residues: 1080 helix: 1.21 (0.27), residues: 402 sheet: -1.99 (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 0.013 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 0.02612 ( 439) hydrogen bonds : angle 4.30173 ( 1320) SS BOND : bond 0.00599 ( 12) SS BOND : angle 1.77947 ( 24) covalent geometry : bond 0.00310 ( 9018) covalent geometry : angle 0.54700 (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 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8622 (pt0) cc_final: 0.8421 (pt0) REVERT: A 397 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6612 (p90) REVERT: C 118 ASP cc_start: 0.7852 (m-30) cc_final: 0.7060 (t0) outliers start: 18 outliers final: 9 residues processed: 126 average time/residue: 0.3625 time to fit residues: 66.3133 Evaluate side-chains 115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 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 402 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.146246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115776 restraints weight = 27692.386| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.13 r_work: 0.3073 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1490 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= 0.131 Angle : 0.545 15.831 12276 Z= 0.299 Chirality : 0.043 0.150 1365 Planarity : 0.004 0.067 1581 Dihedral : 4.432 25.330 1206 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Rotamer: Outliers : 1.53 % Allowed : 8.56 % 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 (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: -1.10 (0.26), residues: 1080 helix: 1.54 (0.28), residues: 384 sheet: -1.99 (0.30), residues: 276 loop : -1.95 (0.26), residues: 420 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 0.013 0.001 PHE B 321 TYR 0.008 0.001 TYR A 199 ARG 0.005 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02552 ( 439) hydrogen bonds : angle 4.22984 ( 1320) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.71242 ( 24) covalent geometry : bond 0.00304 ( 9018) covalent geometry : angle 0.54070 (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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.6738 (p90) REVERT: A 406 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6335 (mp) REVERT: B 397 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6171 (p90) REVERT: C 118 ASP cc_start: 0.7863 (m-30) cc_final: 0.7041 (t0) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 0.3620 time to fit residues: 62.6625 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.140527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109704 restraints weight = 27691.679| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.13 r_work: 0.2996 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9030 Z= 0.239 Angle : 0.614 15.782 12276 Z= 0.337 Chirality : 0.046 0.175 1365 Planarity : 0.005 0.065 1581 Dihedral : 4.743 25.893 1206 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.76 % Favored : 92.69 % Rotamer: Outliers : 1.73 % Allowed : 8.97 % Favored : 89.30 % 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: -1.32 (0.26), residues: 1080 helix: 1.18 (0.27), residues: 390 sheet: -2.17 (0.30), residues: 282 loop : -1.86 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.009 0.002 HIS B 231 PHE 0.023 0.002 PHE B 321 TYR 0.010 0.002 TYR B 371 ARG 0.009 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 439) hydrogen bonds : angle 4.49832 ( 1320) SS BOND : bond 0.00574 ( 12) SS BOND : angle 1.89009 ( 24) covalent geometry : bond 0.00564 ( 9018) covalent geometry : angle 0.60866 (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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.250 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: 0.7938 (OUTLIER) cc_final: 0.6861 (p90) REVERT: A 406 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6292 (mt) REVERT: B 397 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6482 (p90) REVERT: C 118 ASP cc_start: 0.7924 (m-30) cc_final: 0.7086 (t0) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.3509 time to fit residues: 58.7249 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 : 1.251 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.142254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109860 restraints weight = 27685.551| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.22 r_work: 0.3034 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1785 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= 0.152 Angle : 0.563 15.768 12276 Z= 0.308 Chirality : 0.044 0.153 1365 Planarity : 0.005 0.083 1581 Dihedral : 4.640 25.202 1206 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.48 % Favored : 92.96 % Rotamer: Outliers : 1.94 % Allowed : 9.68 % Favored : 88.38 % 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: -1.21 (0.26), residues: 1080 helix: 1.40 (0.27), residues: 387 sheet: -2.39 (0.29), residues: 294 loop : -1.64 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS C 231 PHE 0.013 0.001 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 0.02649 ( 439) hydrogen bonds : angle 4.32325 ( 1320) SS BOND : bond 0.00466 ( 12) SS BOND : angle 1.74031 ( 24) covalent geometry : bond 0.00353 ( 9018) covalent geometry : angle 0.55789 (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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.313 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: 0.8127 (OUTLIER) cc_final: 0.7172 (p90) REVERT: A 406 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6357 (mp) REVERT: B 397 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6448 (p90) REVERT: C 118 ASP cc_start: 0.7889 (m-30) cc_final: 0.7047 (t0) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.3539 time to fit residues: 60.9258 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.143086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112656 restraints weight = 27369.972| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.11 r_work: 0.3017 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9030 Z= 0.176 Angle : 0.573 15.800 12276 Z= 0.314 Chirality : 0.044 0.151 1365 Planarity : 0.005 0.094 1581 Dihedral : 4.656 25.278 1206 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.76 % Favored : 92.69 % Rotamer: Outliers : 1.94 % Allowed : 10.19 % Favored : 87.87 % 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: 1.36 (0.27), residues: 387 sheet: -2.15 (0.30), residues: 282 loop : -1.87 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.006 0.002 HIS B 231 PHE 0.015 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 0.02684 ( 439) hydrogen bonds : angle 4.34048 ( 1320) SS BOND : bond 0.00472 ( 12) SS BOND : angle 1.73357 ( 24) covalent geometry : bond 0.00411 ( 9018) covalent geometry : angle 0.56855 (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 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7128 (p90) REVERT: A 406 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6431 (mp) REVERT: B 397 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.6403 (p90) REVERT: C 118 ASP cc_start: 0.7875 (m-30) cc_final: 0.7017 (t0) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 0.3967 time to fit residues: 66.1859 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 : 1.394 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114509 restraints weight = 27402.884| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.11 r_work: 0.3037 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9030 Z= 0.135 Angle : 0.555 15.808 12276 Z= 0.304 Chirality : 0.044 0.160 1365 Planarity : 0.005 0.084 1581 Dihedral : 4.594 24.623 1206 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.73 % Allowed : 10.40 % Favored : 87.87 % 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: -1.16 (0.26), residues: 1080 helix: 1.47 (0.27), residues: 387 sheet: -2.35 (0.29), residues: 294 loop : -1.64 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS C 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 0.02573 ( 439) hydrogen bonds : angle 4.23861 ( 1320) SS BOND : bond 0.00523 ( 12) SS BOND : angle 1.78529 ( 24) covalent geometry : bond 0.00312 ( 9018) covalent geometry : angle 0.54981 (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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7273 (p90) REVERT: A 406 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6379 (mp) REVERT: B 118 ASP cc_start: 0.7702 (m-30) cc_final: 0.6930 (t0) REVERT: B 397 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.6340 (p90) REVERT: C 118 ASP cc_start: 0.7852 (m-30) cc_final: 0.6983 (t0) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.3549 time to fit residues: 61.0797 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115395 restraints weight = 27459.156| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.11 r_work: 0.3068 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9030 Z= 0.118 Angle : 0.544 15.816 12276 Z= 0.297 Chirality : 0.043 0.144 1365 Planarity : 0.005 0.096 1581 Dihedral : 4.481 23.392 1206 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.06 % Rotamer: Outliers : 1.43 % Allowed : 10.91 % 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: -1.04 (0.26), residues: 1080 helix: 1.61 (0.27), residues: 387 sheet: -2.30 (0.29), residues: 294 loop : -1.61 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.003 0.001 HIS C 231 PHE 0.010 0.001 PHE A 321 TYR 0.009 0.001 TYR A 199 ARG 0.010 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02447 ( 439) hydrogen bonds : angle 4.13221 ( 1320) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.88665 ( 24) covalent geometry : bond 0.00272 ( 9018) covalent geometry : angle 0.53761 (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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.371 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: 0.7228 (p90) REVERT: A 406 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6362 (mp) REVERT: B 118 ASP cc_start: 0.7697 (m-30) cc_final: 0.6909 (t0) REVERT: B 397 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6228 (p90) REVERT: C 118 ASP cc_start: 0.7845 (m-30) cc_final: 0.6976 (t0) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.3660 time to fit residues: 63.4778 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 : 1.298 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.144447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114249 restraints weight = 27389.402| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.11 r_work: 0.3068 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2032 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= 0.154 Angle : 0.564 15.809 12276 Z= 0.308 Chirality : 0.044 0.155 1365 Planarity : 0.005 0.089 1581 Dihedral : 4.632 26.835 1206 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.30 % Favored : 93.15 % Rotamer: Outliers : 1.43 % Allowed : 11.42 % 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 (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: 1.52 (0.27), residues: 387 sheet: -1.99 (0.30), residues: 276 loop : -1.87 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.005 0.001 HIS C 231 PHE 0.013 0.001 PHE A 321 TYR 0.009 0.001 TYR A 199 ARG 0.010 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02583 ( 439) hydrogen bonds : angle 4.20284 ( 1320) SS BOND : bond 0.00445 ( 12) SS BOND : angle 1.89825 ( 24) covalent geometry : bond 0.00358 ( 9018) covalent geometry : angle 0.55821 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8428.83 seconds wall clock time: 143 minutes 39.93 seconds (8619.93 seconds total)