Starting phenix.real_space_refine on Sat May 17 17:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.map" model { file = "/net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yms_39406/05_2025/8yms_39406.cif" } resolution = 3.14 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 7173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 15975 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "C" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "B" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5325 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Time building chain proxies: 8.55, per 1000 atoms: 0.54 Number of scatterers: 15975 At special positions: 0 Unit cell: (98.58, 98.58, 122.76, 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 7173 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 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 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 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: 4.59 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: 29 helices and 12 sheets defined 35.9% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 53 through 83 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.510A pdb=" N ASP A 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 133 " --> pdb=" O PHE A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 133' Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.286A pdb=" N SER A 237 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.588A pdb=" N TYR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.775A pdb=" N ASN A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.508A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.545A pdb=" N SER C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.584A pdb=" N ASP C 132 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 133 " --> pdb=" O PHE C 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 133' Processing helix chain 'C' and resid 233 through 239 removed outlier: 4.193A pdb=" N SER C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 296 removed outlier: 3.603A pdb=" N TYR C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.636A pdb=" N ASN C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.512A pdb=" N GLU C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'B' and resid 54 through 83 removed outlier: 3.642A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.581A pdb=" N ASP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 133 " --> pdb=" O PHE B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 233 through 239 removed outlier: 4.107A pdb=" N SER B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 239' Processing helix chain 'B' and resid 275 through 296 removed outlier: 3.565A pdb=" N TYR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.823A pdb=" N ASN B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.589A pdb=" N GLU B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 403 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 3.639A pdb=" N ALA A 87 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 372 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 254 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR A 366 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.049A 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: 3.639A pdb=" N ALA A 87 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 372 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR A 371 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N PHE A 260 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 255 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET A 351 " --> pdb=" O ALA A 255 " (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: 7.047A pdb=" N GLN A 187 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 92 removed outlier: 3.709A pdb=" N ALA C 87 " --> pdb=" O TYR C 378 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C 255 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 351 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'C' and resid 179 through 183 removed outlier: 7.008A pdb=" N GLN C 187 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 92 removed outlier: 3.758A pdb=" N ALA B 87 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 254 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR B 366 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE B 256 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 86 through 92 removed outlier: 3.758A pdb=" N ALA B 87 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA B 255 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET B 351 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'B' and resid 179 through 183 removed outlier: 7.133A pdb=" N GLN B 187 " --> pdb=" O PRO B 107 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1170 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: 5.55 Time building geometry restraints manager: 5.42 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: 7170 1.03 - 1.23: 150 1.23 - 1.43: 3751 1.43 - 1.62: 5039 1.62 - 1.82: 81 Bond restraints: 16191 Sorted by residual: bond pdb=" C MET A 304 " pdb=" N ARG A 305 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.47e-02 4.63e+03 9.78e+00 bond pdb=" C MET C 304 " pdb=" N ARG C 305 " ideal model delta sigma weight residual 1.329 1.354 -0.026 1.86e-02 2.89e+03 1.91e+00 bond pdb=" C MET B 304 " pdb=" N ARG B 305 " ideal model delta sigma weight residual 1.329 1.351 -0.023 1.86e-02 2.89e+03 1.49e+00 bond pdb=" CA CYS B 311 " pdb=" C CYS B 311 " ideal model delta sigma weight residual 1.532 1.521 0.011 9.60e-03 1.09e+04 1.42e+00 bond pdb=" N ILE C 347 " pdb=" CA ILE C 347 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.34e+00 ... (remaining 16186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.86: 28394 10.86 - 21.72: 16 21.72 - 32.58: 86 32.58 - 43.44: 22 43.44 - 54.30: 12 Bond angle restraints: 28530 Sorted by residual: angle pdb=" C ILE A 291 " pdb=" N TYR A 292 " pdb=" H TYR A 292 " ideal model delta sigma weight residual 124.93 70.63 54.30 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C ILE B 291 " pdb=" N TYR B 292 " pdb=" H TYR B 292 " ideal model delta sigma weight residual 125.00 70.72 54.28 3.00e+00 1.11e-01 3.27e+02 angle pdb=" C ILE C 291 " pdb=" N TYR C 292 " pdb=" H TYR C 292 " ideal model delta sigma weight residual 124.93 70.66 54.27 3.00e+00 1.11e-01 3.27e+02 angle pdb=" C THR A 114 " pdb=" N ILE A 115 " pdb=" H ILE A 115 " ideal model delta sigma weight residual 124.87 70.68 54.19 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C THR B 114 " pdb=" N ILE B 115 " pdb=" H ILE B 115 " ideal model delta sigma weight residual 124.87 70.70 54.17 3.00e+00 1.11e-01 3.26e+02 ... (remaining 28525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7182 17.79 - 35.58: 506 35.58 - 53.38: 125 53.38 - 71.17: 26 71.17 - 88.96: 21 Dihedral angle restraints: 7860 sinusoidal: 4116 harmonic: 3744 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 179.23 -86.23 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS C 282 " pdb=" SG CYS C 282 " pdb=" SG CYS C 337 " pdb=" CB CYS C 337 " ideal model delta sinusoidal sigma weight residual 93.00 167.50 -74.50 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CA TYR A 139 " pdb=" C TYR A 139 " pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1276 0.097 - 0.194: 80 0.194 - 0.290: 0 0.290 - 0.387: 3 0.387 - 0.484: 6 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" C PRO B 272 " pdb=" CB PRO B 272 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" C PRO C 272 " pdb=" CB PRO C 272 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA PRO A 272 " pdb=" N PRO A 272 " pdb=" C PRO A 272 " pdb=" CB PRO A 272 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 1362 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C LYS C 127 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS C 127 " -0.015 2.00e-02 2.50e+03 pdb=" N MET C 128 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 305 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO C 306 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 306 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 306 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 305 " 0.027 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 306 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " 0.023 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 673 2.16 - 2.77: 28545 2.77 - 3.38: 42795 3.38 - 3.99: 56142 3.99 - 4.60: 87318 Nonbonded interactions: 215473 Sorted by model distance: nonbonded pdb=" H TYR A 292 " pdb=" HA TYR A 292 " model vdw 1.545 1.816 nonbonded pdb=" H ILE A 115 " pdb=" HA ILE A 115 " model vdw 1.551 1.816 nonbonded pdb=" H ILE B 115 " pdb=" HA ILE B 115 " model vdw 1.551 1.816 nonbonded pdb=" H ILE C 115 " pdb=" HA ILE C 115 " model vdw 1.553 1.816 nonbonded pdb=" H TYR B 292 " pdb=" HA TYR B 292 " model vdw 1.557 1.816 ... (remaining 215468 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: 0.04 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: 0.740 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: 37.840 Find NCS groups from input model: 0.420 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 0.046 9030 Z= 0.180 Angle : 0.807 11.155 12276 Z= 0.511 Chirality : 0.056 0.484 1365 Planarity : 0.004 0.048 1581 Dihedral : 13.521 88.961 3306 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.70 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1080 helix: 1.15 (0.29), residues: 360 sheet: -2.14 (0.31), residues: 267 loop : -2.97 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.009 0.001 HIS B 229 PHE 0.024 0.002 PHE A 350 TYR 0.016 0.001 TYR A 81 ARG 0.012 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.19585 ( 400) hydrogen bonds : angle 8.70705 ( 1170) SS BOND : bond 0.00376 ( 12) SS BOND : angle 0.82178 ( 24) covalent geometry : bond 0.00340 ( 9018) covalent geometry : angle 0.80683 (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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.7223 (pp) cc_final: 0.6637 (mt) REVERT: C 342 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5920 (pm20) REVERT: C 394 LEU cc_start: 0.7301 (pp) cc_final: 0.6803 (mt) REVERT: B 278 GLU cc_start: 0.8076 (tt0) cc_final: 0.7692 (tt0) REVERT: B 394 LEU cc_start: 0.7213 (pp) cc_final: 0.6707 (mt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4982 time to fit residues: 88.9703 Evaluate side-chains 95 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 4.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS B 72 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.188731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154905 restraints weight = 25153.036| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.34 r_work: 0.3614 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9030 Z= 0.156 Angle : 0.688 11.743 12276 Z= 0.392 Chirality : 0.054 0.390 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.934 31.738 1206 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.06 % Favored : 91.30 % Rotamer: Outliers : 0.92 % Allowed : 5.71 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.85 (0.26), residues: 1080 helix: 1.29 (0.29), residues: 369 sheet: -2.02 (0.31), residues: 267 loop : -2.96 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.007 0.001 HIS B 229 PHE 0.015 0.001 PHE C 256 TYR 0.009 0.001 TYR A 170 ARG 0.002 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 400) hydrogen bonds : angle 5.96276 ( 1170) SS BOND : bond 0.00406 ( 12) SS BOND : angle 0.86746 ( 24) covalent geometry : bond 0.00349 ( 9018) covalent geometry : angle 0.68772 (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 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7964 (mtp) cc_final: 0.7607 (mtt) REVERT: A 394 LEU cc_start: 0.7837 (pp) cc_final: 0.7141 (mt) REVERT: C 254 PHE cc_start: 0.7690 (p90) cc_final: 0.7437 (p90) REVERT: C 342 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6207 (pm20) REVERT: C 394 LEU cc_start: 0.7875 (pp) cc_final: 0.7212 (mt) REVERT: B 278 GLU cc_start: 0.8347 (tt0) cc_final: 0.7970 (tt0) REVERT: B 394 LEU cc_start: 0.7752 (pp) cc_final: 0.7099 (mt) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.5423 time to fit residues: 81.6187 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152602 restraints weight = 25046.471| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.32 r_work: 0.3564 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9030 Z= 0.136 Angle : 0.657 11.775 12276 Z= 0.372 Chirality : 0.053 0.390 1365 Planarity : 0.004 0.035 1581 Dihedral : 5.697 31.874 1206 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.43 % Favored : 90.93 % Rotamer: Outliers : 1.22 % Allowed : 8.05 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: 1.52 (0.29), residues: 366 sheet: -2.00 (0.30), residues: 276 loop : -2.85 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.008 0.001 HIS C 229 PHE 0.013 0.001 PHE C 256 TYR 0.010 0.001 TYR A 139 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 400) hydrogen bonds : angle 5.20013 ( 1170) SS BOND : bond 0.00406 ( 12) SS BOND : angle 0.84856 ( 24) covalent geometry : bond 0.00302 ( 9018) covalent geometry : angle 0.65648 (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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.5990 (ttm) cc_final: 0.5740 (tpt) REVERT: A 394 LEU cc_start: 0.7838 (pp) cc_final: 0.7151 (mt) REVERT: C 394 LEU cc_start: 0.7852 (pp) cc_final: 0.7243 (mt) REVERT: B 76 MET cc_start: 0.7910 (mtp) cc_final: 0.7565 (mtt) REVERT: B 394 LEU cc_start: 0.7755 (pp) cc_final: 0.7138 (mt) outliers start: 12 outliers final: 11 residues processed: 120 average time/residue: 0.5525 time to fit residues: 85.2837 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.187115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154851 restraints weight = 24948.161| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.25 r_work: 0.3572 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2280 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= 0.152 Angle : 0.658 11.753 12276 Z= 0.373 Chirality : 0.054 0.390 1365 Planarity : 0.004 0.037 1581 Dihedral : 5.628 31.796 1206 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.80 % Favored : 90.65 % Rotamer: Outliers : 1.43 % Allowed : 9.07 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.66 (0.26), residues: 1080 helix: 1.42 (0.29), residues: 375 sheet: -2.09 (0.30), residues: 285 loop : -2.74 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.006 0.001 HIS C 229 PHE 0.015 0.001 PHE C 256 TYR 0.011 0.001 TYR A 139 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 400) hydrogen bonds : angle 4.93338 ( 1170) SS BOND : bond 0.00423 ( 12) SS BOND : angle 0.97450 ( 24) covalent geometry : bond 0.00344 ( 9018) covalent geometry : angle 0.65739 (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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5615 (tt0) cc_final: 0.4801 (mp0) REVERT: A 111 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6754 (tp40) REVERT: A 394 LEU cc_start: 0.7849 (pp) cc_final: 0.7161 (mt) REVERT: C 342 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6053 (pm20) REVERT: C 394 LEU cc_start: 0.7844 (pp) cc_final: 0.7234 (mt) REVERT: B 76 MET cc_start: 0.7970 (mtp) cc_final: 0.7631 (mtt) REVERT: B 394 LEU cc_start: 0.7803 (pp) cc_final: 0.7192 (mt) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.5189 time to fit residues: 80.2291 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146243 restraints weight = 25598.935| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.30 r_work: 0.3527 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2683 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= 0.192 Angle : 0.679 11.396 12276 Z= 0.385 Chirality : 0.054 0.386 1365 Planarity : 0.004 0.040 1581 Dihedral : 5.770 32.766 1206 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.07 % Favored : 90.37 % 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 : 0.29 % 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: -1.76 (0.26), residues: 1080 helix: 1.43 (0.29), residues: 366 sheet: -2.08 (0.30), residues: 285 loop : -2.86 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.006 0.001 HIS C 233 PHE 0.018 0.002 PHE C 256 TYR 0.011 0.001 TYR C 378 ARG 0.002 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 400) hydrogen bonds : angle 4.86234 ( 1170) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.13806 ( 24) covalent geometry : bond 0.00440 ( 9018) covalent geometry : angle 0.67802 (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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5614 (tt0) cc_final: 0.4820 (mp0) REVERT: A 119 MET cc_start: 0.6479 (mmm) cc_final: 0.6104 (tpp) REVERT: A 394 LEU cc_start: 0.7928 (pp) cc_final: 0.7152 (mt) REVERT: C 129 LYS cc_start: 0.8043 (mttt) cc_final: 0.7819 (mttp) REVERT: C 394 LEU cc_start: 0.7909 (pp) cc_final: 0.7274 (mt) REVERT: B 128 MET cc_start: 0.6640 (mpp) cc_final: 0.6344 (mpp) REVERT: B 278 GLU cc_start: 0.8410 (tt0) cc_final: 0.8136 (tt0) REVERT: B 394 LEU cc_start: 0.7873 (pp) cc_final: 0.7225 (mt) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.5101 time to fit residues: 79.6647 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145927 restraints weight = 25213.903| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.18 r_work: 0.3490 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2859 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 : 0.641 11.603 12276 Z= 0.362 Chirality : 0.053 0.386 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.540 31.724 1206 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 2.14 % Allowed : 11.01 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.66 (0.26), residues: 1080 helix: 1.48 (0.28), residues: 375 sheet: -1.97 (0.30), residues: 282 loop : -2.90 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.007 0.001 HIS C 229 PHE 0.014 0.001 PHE C 256 TYR 0.013 0.001 TYR B 139 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 400) hydrogen bonds : angle 4.64564 ( 1170) SS BOND : bond 0.00394 ( 12) SS BOND : angle 0.90907 ( 24) covalent geometry : bond 0.00287 ( 9018) covalent geometry : angle 0.64017 (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 139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5320 (tt0) cc_final: 0.4729 (mp0) REVERT: A 119 MET cc_start: 0.6477 (mmm) cc_final: 0.6119 (tpp) REVERT: A 394 LEU cc_start: 0.7821 (pp) cc_final: 0.7138 (mt) REVERT: C 394 LEU cc_start: 0.7750 (pp) cc_final: 0.7162 (mt) REVERT: B 128 MET cc_start: 0.6545 (mpp) cc_final: 0.6269 (mpp) REVERT: B 278 GLU cc_start: 0.8149 (tt0) cc_final: 0.7896 (tt0) REVERT: B 394 LEU cc_start: 0.7807 (pp) cc_final: 0.7215 (mt) outliers start: 21 outliers final: 14 residues processed: 129 average time/residue: 0.4925 time to fit residues: 84.1887 Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.177875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145250 restraints weight = 25630.798| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.36 r_work: 0.3539 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9030 Z= 0.133 Angle : 0.663 14.390 12276 Z= 0.370 Chirality : 0.054 0.385 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.421 31.520 1206 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.15 % Favored : 91.20 % Rotamer: Outliers : 1.94 % Allowed : 11.62 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.55 (0.26), residues: 1080 helix: 1.55 (0.28), residues: 375 sheet: -1.91 (0.30), residues: 282 loop : -2.82 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.007 0.001 HIS C 229 PHE 0.014 0.001 PHE A 286 TYR 0.014 0.001 TYR A 139 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 400) hydrogen bonds : angle 4.50360 ( 1170) SS BOND : bond 0.00694 ( 12) SS BOND : angle 1.38476 ( 24) covalent geometry : bond 0.00294 ( 9018) covalent geometry : angle 0.66053 (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 136 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5358 (tt0) cc_final: 0.4798 (mp0) REVERT: A 119 MET cc_start: 0.6433 (mmm) cc_final: 0.6112 (tpp) REVERT: A 394 LEU cc_start: 0.7865 (pp) cc_final: 0.7190 (mt) REVERT: C 378 TYR cc_start: 0.8628 (p90) cc_final: 0.8362 (p90) REVERT: C 394 LEU cc_start: 0.7740 (pp) cc_final: 0.7112 (mt) REVERT: B 128 MET cc_start: 0.6516 (mpp) cc_final: 0.6232 (mpp) REVERT: B 394 LEU cc_start: 0.7809 (pp) cc_final: 0.7232 (mt) outliers start: 19 outliers final: 16 residues processed: 126 average time/residue: 0.4830 time to fit residues: 80.5544 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 102 optimal weight: 0.0670 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149582 restraints weight = 25306.772| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.34 r_work: 0.3607 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9030 Z= 0.106 Angle : 0.627 11.799 12276 Z= 0.353 Chirality : 0.053 0.383 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.179 29.988 1206 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.22 % Favored : 92.22 % Rotamer: Outliers : 1.73 % Allowed : 12.03 % Favored : 86.24 % 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: -1.33 (0.26), residues: 1080 helix: 1.82 (0.29), residues: 369 sheet: -1.77 (0.30), residues: 282 loop : -2.74 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.007 0.001 HIS C 229 PHE 0.013 0.001 PHE A 286 TYR 0.016 0.001 TYR B 139 ARG 0.002 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 400) hydrogen bonds : angle 4.32643 ( 1170) SS BOND : bond 0.00401 ( 12) SS BOND : angle 0.82658 ( 24) covalent geometry : bond 0.00233 ( 9018) covalent geometry : angle 0.62615 (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 136 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5058 (tt0) cc_final: 0.4730 (mp0) REVERT: A 119 MET cc_start: 0.6356 (mmm) cc_final: 0.6059 (tpp) REVERT: A 394 LEU cc_start: 0.7775 (pp) cc_final: 0.7140 (mt) REVERT: C 378 TYR cc_start: 0.8557 (p90) cc_final: 0.8305 (p90) REVERT: C 394 LEU cc_start: 0.7645 (pp) cc_final: 0.7074 (mt) REVERT: B 89 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7595 (ptt180) REVERT: B 128 MET cc_start: 0.6523 (mpp) cc_final: 0.6164 (mpp) REVERT: B 278 GLU cc_start: 0.8238 (tt0) cc_final: 0.7980 (tt0) REVERT: B 394 LEU cc_start: 0.7742 (pp) cc_final: 0.7206 (mt) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.5553 time to fit residues: 90.2117 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 : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.176867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143569 restraints weight = 25448.413| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.36 r_work: 0.3536 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9030 Z= 0.178 Angle : 0.665 11.574 12276 Z= 0.375 Chirality : 0.054 0.384 1365 Planarity : 0.004 0.047 1581 Dihedral : 5.416 30.603 1206 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.43 % Favored : 91.02 % Rotamer: Outliers : 1.83 % Allowed : 11.93 % Favored : 86.24 % 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: -1.45 (0.26), residues: 1080 helix: 1.64 (0.29), residues: 366 sheet: -1.76 (0.31), residues: 276 loop : -2.74 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.003 0.001 HIS C 233 PHE 0.017 0.002 PHE A 286 TYR 0.011 0.001 TYR A 139 ARG 0.002 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 400) hydrogen bonds : angle 4.45592 ( 1170) SS BOND : bond 0.00431 ( 12) SS BOND : angle 1.17078 ( 24) covalent geometry : bond 0.00414 ( 9018) covalent geometry : angle 0.66371 (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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5378 (tt0) cc_final: 0.4798 (mp0) REVERT: A 119 MET cc_start: 0.6564 (mmm) cc_final: 0.6263 (tpp) REVERT: A 394 LEU cc_start: 0.7907 (pp) cc_final: 0.7183 (mt) REVERT: C 378 TYR cc_start: 0.8657 (p90) cc_final: 0.8408 (p90) REVERT: C 394 LEU cc_start: 0.7745 (pp) cc_final: 0.7152 (mt) REVERT: B 84 GLU cc_start: 0.5701 (tt0) cc_final: 0.4848 (mp0) REVERT: B 128 MET cc_start: 0.6541 (mpp) cc_final: 0.6231 (mpp) REVERT: B 394 LEU cc_start: 0.7816 (pp) cc_final: 0.7224 (mt) outliers start: 18 outliers final: 17 residues processed: 118 average time/residue: 0.4921 time to fit residues: 76.4839 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 : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.181177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147998 restraints weight = 25320.751| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.37 r_work: 0.3574 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9030 Z= 0.101 Angle : 0.625 11.482 12276 Z= 0.350 Chirality : 0.052 0.381 1365 Planarity : 0.003 0.045 1581 Dihedral : 5.112 28.733 1206 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.04 % Favored : 92.41 % Rotamer: Outliers : 1.12 % Allowed : 12.84 % Favored : 86.03 % 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: 1.86 (0.29), residues: 366 sheet: -1.68 (0.31), residues: 282 loop : -2.68 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.008 0.001 HIS C 229 PHE 0.014 0.001 PHE A 286 TYR 0.016 0.001 TYR A 139 ARG 0.002 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 400) hydrogen bonds : angle 4.27527 ( 1170) SS BOND : bond 0.00341 ( 12) SS BOND : angle 0.80911 ( 24) covalent geometry : bond 0.00223 ( 9018) covalent geometry : angle 0.62430 (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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6479 (mmm) cc_final: 0.6199 (tpp) REVERT: A 394 LEU cc_start: 0.7748 (pp) cc_final: 0.7122 (mt) REVERT: C 238 ARG cc_start: 0.7570 (mpt-90) cc_final: 0.7349 (mmt90) REVERT: C 378 TYR cc_start: 0.8523 (p90) cc_final: 0.8291 (p90) REVERT: C 394 LEU cc_start: 0.7626 (pp) cc_final: 0.7052 (mt) REVERT: B 84 GLU cc_start: 0.5375 (tt0) cc_final: 0.4815 (mp0) REVERT: B 128 MET cc_start: 0.6513 (mpp) cc_final: 0.6189 (mpp) REVERT: B 278 GLU cc_start: 0.8199 (tt0) cc_final: 0.7994 (tt0) REVERT: B 394 LEU cc_start: 0.7707 (pp) cc_final: 0.7168 (mt) outliers start: 11 outliers final: 11 residues processed: 119 average time/residue: 0.5072 time to fit residues: 79.2201 Evaluate side-chains 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.179097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.146399 restraints weight = 25266.067| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.35 r_work: 0.3582 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9030 Z= 0.117 Angle : 0.626 11.635 12276 Z= 0.351 Chirality : 0.053 0.382 1365 Planarity : 0.003 0.046 1581 Dihedral : 5.080 28.181 1206 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.87 % Favored : 91.67 % Rotamer: Outliers : 1.43 % Allowed : 13.46 % Favored : 85.12 % 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: 1.87 (0.29), residues: 366 sheet: -1.54 (0.31), residues: 276 loop : -2.70 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.006 0.001 HIS C 229 PHE 0.015 0.001 PHE B 286 TYR 0.014 0.001 TYR A 139 ARG 0.002 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 400) hydrogen bonds : angle 4.24855 ( 1170) SS BOND : bond 0.00379 ( 12) SS BOND : angle 0.97633 ( 24) covalent geometry : bond 0.00264 ( 9018) covalent geometry : angle 0.62486 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8370.03 seconds wall clock time: 144 minutes 22.79 seconds (8662.79 seconds total)