Starting phenix.real_space_refine on Sat Jun 14 07:57:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yms_39406/06_2025/8yms_39406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yms_39406/06_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_39406/06_2025/8yms_39406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yms_39406/06_2025/8yms_39406.map" model { file = "/net/cci-nas-00/data/ceres_data/8yms_39406/06_2025/8yms_39406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yms_39406/06_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-5710/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: 9.63, per 1000 atoms: 0.60 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: 4.33 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: 1.35 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: 6.02 Time building geometry restraints manager: 5.19 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.560 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- 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 : 1.303 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: 0.4977 time to fit residues: 88.6062 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 : 1.318 ------------------------------------------------------------------------------- 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: 4.84 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 1.341 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: 0.7967 (mtp) cc_final: 0.7611 (mtt) REVERT: A 394 LEU cc_start: 0.7844 (pp) cc_final: 0.7146 (mt) REVERT: C 254 PHE cc_start: 0.7692 (p90) cc_final: 0.7440 (p90) REVERT: C 342 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6209 (pm20) REVERT: C 394 LEU cc_start: 0.7882 (pp) cc_final: 0.7216 (mt) REVERT: B 278 GLU cc_start: 0.8347 (tt0) cc_final: 0.7969 (tt0) REVERT: B 394 LEU cc_start: 0.7762 (pp) cc_final: 0.7105 (mt) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.5510 time to fit residues: 83.2953 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 : 1.356 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4050 r_free = 0.4050 target = 0.185852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152686 restraints weight = 25037.067| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.32 r_work: 0.3611 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1819 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= 0.135 Angle : 0.658 11.773 12276 Z= 0.373 Chirality : 0.053 0.391 1365 Planarity : 0.004 0.035 1581 Dihedral : 5.707 31.837 1206 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.33 % Favored : 91.02 % Rotamer: Outliers : 0.92 % Allowed : 7.85 % Favored : 91.23 % 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: -1.69 (0.26), residues: 1080 helix: 1.51 (0.29), residues: 366 sheet: -2.02 (0.30), residues: 276 loop : -2.86 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.03503 ( 400) hydrogen bonds : angle 5.26064 ( 1170) SS BOND : bond 0.00397 ( 12) SS BOND : angle 0.83391 ( 24) covalent geometry : bond 0.00300 ( 9018) covalent geometry : angle 0.65731 (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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.278 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 394 LEU cc_start: 0.7834 (pp) cc_final: 0.7151 (mt) REVERT: C 342 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6246 (pm20) REVERT: C 394 LEU cc_start: 0.7857 (pp) cc_final: 0.7245 (mt) REVERT: B 278 GLU cc_start: 0.8269 (tt0) cc_final: 0.7888 (tt0) REVERT: B 394 LEU cc_start: 0.7750 (pp) cc_final: 0.7131 (mt) outliers start: 9 outliers final: 8 residues processed: 121 average time/residue: 0.5588 time to fit residues: 86.8422 Evaluate side-chains 107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE 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 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: 0.2980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.190871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158412 restraints weight = 24826.566| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.26 r_work: 0.3611 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9030 Z= 0.113 Angle : 0.634 11.792 12276 Z= 0.360 Chirality : 0.053 0.387 1365 Planarity : 0.004 0.038 1581 Dihedral : 5.472 31.004 1206 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 1.33 % Allowed : 8.46 % Favored : 90.21 % 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: -1.57 (0.26), residues: 1080 helix: 1.54 (0.29), residues: 375 sheet: -2.07 (0.30), residues: 285 loop : -2.72 (0.26), residues: 420 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 0.011 0.001 PHE C 256 TYR 0.011 0.001 TYR A 139 ARG 0.001 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 400) hydrogen bonds : angle 4.92426 ( 1170) SS BOND : bond 0.00381 ( 12) SS BOND : angle 0.80200 ( 24) covalent geometry : bond 0.00248 ( 9018) covalent geometry : angle 0.63394 (12252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.226 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: 0.5497 (tt0) cc_final: 0.4766 (mp0) REVERT: A 394 LEU cc_start: 0.7788 (pp) cc_final: 0.7142 (mt) REVERT: C 342 GLU cc_start: 0.6710 (mt-10) cc_final: 0.5996 (pm20) REVERT: C 394 LEU cc_start: 0.7865 (pp) cc_final: 0.7229 (mt) REVERT: B 76 MET cc_start: 0.7877 (mtp) cc_final: 0.7531 (mtt) REVERT: B 394 LEU cc_start: 0.7743 (pp) cc_final: 0.7162 (mt) outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 0.5035 time to fit residues: 81.0968 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 156 SER 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 156 SER 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: 0.7980 chunk 10 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.182868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149990 restraints weight = 25468.012| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.32 r_work: 0.3565 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2382 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= 0.134 Angle : 0.638 11.464 12276 Z= 0.360 Chirality : 0.053 0.391 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.431 30.791 1206 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 1.73 % Allowed : 9.48 % Favored : 88.79 % 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: -1.56 (0.26), residues: 1080 helix: 1.57 (0.29), residues: 375 sheet: -2.01 (0.30), residues: 285 loop : -2.78 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.005 0.001 HIS C 229 PHE 0.012 0.001 PHE C 256 TYR 0.012 0.001 TYR A 139 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 400) hydrogen bonds : angle 4.74170 ( 1170) SS BOND : bond 0.00391 ( 12) SS BOND : angle 0.92637 ( 24) covalent geometry : bond 0.00302 ( 9018) covalent geometry : angle 0.63683 (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 136 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.427 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: 0.5471 (tt0) cc_final: 0.4751 (mp0) REVERT: A 111 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6941 (tp40) REVERT: A 119 MET cc_start: 0.6377 (mmm) cc_final: 0.5999 (tpp) REVERT: A 394 LEU cc_start: 0.7837 (pp) cc_final: 0.7144 (mt) REVERT: C 394 LEU cc_start: 0.7826 (pp) cc_final: 0.7234 (mt) REVERT: B 76 MET cc_start: 0.7903 (mtp) cc_final: 0.7549 (mtt) REVERT: B 129 LYS cc_start: 0.8158 (mttp) cc_final: 0.7888 (mttp) REVERT: B 278 GLU cc_start: 0.8287 (tt0) cc_final: 0.7897 (tt0) REVERT: B 394 LEU cc_start: 0.7790 (pp) cc_final: 0.7197 (mt) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.5625 time to fit residues: 96.2283 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 156 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain C residue 67 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 67 PHE Chi-restraints excluded: chain B residue 80 ASP 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: 0.0170 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.175727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144951 restraints weight = 25266.108| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.15 r_work: 0.3483 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9030 Z= 0.179 Angle : 0.666 11.622 12276 Z= 0.376 Chirality : 0.054 0.386 1365 Planarity : 0.004 0.045 1581 Dihedral : 5.593 31.669 1206 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.24 % Favored : 91.20 % Rotamer: Outliers : 2.14 % Allowed : 10.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.67 (0.26), residues: 1080 helix: 1.44 (0.28), residues: 375 sheet: -1.97 (0.30), residues: 282 loop : -2.87 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.005 0.001 HIS C 233 PHE 0.018 0.002 PHE C 256 TYR 0.012 0.001 TYR C 378 ARG 0.002 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 400) hydrogen bonds : angle 4.72126 ( 1170) SS BOND : bond 0.00468 ( 12) SS BOND : angle 1.13462 ( 24) covalent geometry : bond 0.00413 ( 9018) covalent geometry : angle 0.66433 (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 134 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.226 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: 0.5534 (tt0) cc_final: 0.4809 (mp0) REVERT: A 119 MET cc_start: 0.6472 (mmm) cc_final: 0.6118 (tpp) REVERT: A 394 LEU cc_start: 0.7881 (pp) cc_final: 0.7142 (mt) REVERT: C 129 LYS cc_start: 0.8107 (mttt) cc_final: 0.7847 (mttp) REVERT: C 394 LEU cc_start: 0.7809 (pp) cc_final: 0.7212 (mt) REVERT: B 128 MET cc_start: 0.6562 (mpp) cc_final: 0.6281 (mpp) REVERT: B 129 LYS cc_start: 0.8065 (mttp) cc_final: 0.7847 (mttp) REVERT: B 278 GLU cc_start: 0.8231 (tt0) cc_final: 0.7839 (tt0) REVERT: B 394 LEU cc_start: 0.7794 (pp) cc_final: 0.7172 (mt) outliers start: 21 outliers final: 18 residues processed: 123 average time/residue: 0.5012 time to fit residues: 82.1133 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 372 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 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 Chi-restraints excluded: chain B residue 274 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 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 = 0.3950 r_free = 0.3950 target = 0.176876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144011 restraints weight = 25641.366| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.34 r_work: 0.3512 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3071 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= 0.178 Angle : 0.671 11.529 12276 Z= 0.378 Chirality : 0.054 0.386 1365 Planarity : 0.004 0.046 1581 Dihedral : 5.629 32.357 1206 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 2.45 % Allowed : 10.81 % Favored : 86.75 % 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: 1.53 (0.29), residues: 366 sheet: -1.98 (0.30), residues: 282 loop : -2.86 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS C 229 PHE 0.017 0.002 PHE C 256 TYR 0.012 0.001 TYR C 378 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 400) hydrogen bonds : angle 4.68300 ( 1170) SS BOND : bond 0.00438 ( 12) SS BOND : angle 1.12181 ( 24) covalent geometry : bond 0.00411 ( 9018) covalent geometry : angle 0.67007 (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 141 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5400 (tt0) cc_final: 0.4797 (mp0) REVERT: A 119 MET cc_start: 0.6502 (mmm) cc_final: 0.6163 (tpp) REVERT: A 394 LEU cc_start: 0.7879 (pp) cc_final: 0.7161 (mt) REVERT: C 129 LYS cc_start: 0.8047 (mttt) cc_final: 0.7795 (mttp) REVERT: C 394 LEU cc_start: 0.7731 (pp) cc_final: 0.7152 (mt) REVERT: B 128 MET cc_start: 0.6516 (mpp) cc_final: 0.6235 (mpp) REVERT: B 278 GLU cc_start: 0.8184 (tt0) cc_final: 0.7759 (tt0) REVERT: B 394 LEU cc_start: 0.7794 (pp) cc_final: 0.7186 (mt) outliers start: 24 outliers final: 18 residues processed: 128 average time/residue: 0.4881 time to fit residues: 82.7106 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 274 VAL 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: 0.6980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 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 111 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 = 0.3964 r_free = 0.3964 target = 0.178242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145476 restraints weight = 25473.841| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.35 r_work: 0.3546 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3234 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= 0.130 Angle : 0.643 11.667 12276 Z= 0.362 Chirality : 0.053 0.385 1365 Planarity : 0.004 0.045 1581 Dihedral : 5.433 31.284 1206 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.24 % Favored : 91.20 % Rotamer: Outliers : 2.04 % Allowed : 11.42 % Favored : 86.54 % 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: -1.50 (0.26), residues: 1080 helix: 1.69 (0.29), residues: 366 sheet: -1.88 (0.30), residues: 282 loop : -2.80 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.006 0.001 HIS C 229 PHE 0.014 0.001 PHE C 256 TYR 0.014 0.001 TYR B 139 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 400) hydrogen bonds : angle 4.54989 ( 1170) SS BOND : bond 0.00457 ( 12) SS BOND : angle 1.14709 ( 24) covalent geometry : bond 0.00293 ( 9018) covalent geometry : angle 0.64178 (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 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.246 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: 0.5311 (tt0) cc_final: 0.4832 (mp0) REVERT: A 119 MET cc_start: 0.6391 (mmm) cc_final: 0.6084 (tpp) REVERT: A 394 LEU cc_start: 0.7850 (pp) cc_final: 0.7174 (mt) REVERT: C 129 LYS cc_start: 0.8071 (mttt) cc_final: 0.7851 (mttp) REVERT: C 277 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 394 LEU cc_start: 0.7721 (pp) cc_final: 0.7111 (mt) REVERT: B 128 MET cc_start: 0.6500 (mpp) cc_final: 0.6193 (mpp) REVERT: B 278 GLU cc_start: 0.8147 (tt0) cc_final: 0.7694 (tt0) REVERT: B 394 LEU cc_start: 0.7784 (pp) cc_final: 0.7212 (mt) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.5214 time to fit residues: 84.0914 Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 78 VAL 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 80 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 31 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: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 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 = 0.3927 r_free = 0.3927 target = 0.174833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142050 restraints weight = 25521.507| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.33 r_work: 0.3542 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9030 Z= 0.193 Angle : 0.675 11.526 12276 Z= 0.380 Chirality : 0.054 0.383 1365 Planarity : 0.004 0.047 1581 Dihedral : 5.588 31.785 1206 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.61 % Favored : 90.83 % Rotamer: Outliers : 2.24 % Allowed : 11.82 % Favored : 85.93 % 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: -1.59 (0.26), residues: 1080 helix: 1.60 (0.28), residues: 366 sheet: -1.91 (0.30), residues: 282 loop : -2.85 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.004 0.001 HIS C 233 PHE 0.017 0.002 PHE C 256 TYR 0.011 0.001 TYR C 378 ARG 0.003 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 400) hydrogen bonds : angle 4.61287 ( 1170) SS BOND : bond 0.00553 ( 12) SS BOND : angle 1.36269 ( 24) covalent geometry : bond 0.00452 ( 9018) covalent geometry : angle 0.67292 (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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.432 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: 0.5439 (tt0) cc_final: 0.4865 (mp0) REVERT: A 119 MET cc_start: 0.6563 (mmm) cc_final: 0.6273 (tpp) REVERT: A 394 LEU cc_start: 0.7942 (pp) cc_final: 0.7216 (mt) REVERT: C 128 MET cc_start: 0.6821 (mpp) cc_final: 0.6586 (mpp) REVERT: C 129 LYS cc_start: 0.8097 (mttt) cc_final: 0.7878 (mttp) REVERT: C 394 LEU cc_start: 0.7782 (pp) cc_final: 0.7197 (mt) REVERT: B 128 MET cc_start: 0.6626 (mpp) cc_final: 0.6305 (mpp) REVERT: B 278 GLU cc_start: 0.8161 (tt0) cc_final: 0.7707 (tt0) REVERT: B 394 LEU cc_start: 0.7850 (pp) cc_final: 0.7246 (mt) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.5223 time to fit residues: 85.8405 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 78 VAL 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 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 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: 1.9990 chunk 68 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 ** 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 = 0.3984 r_free = 0.3984 target = 0.179863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147104 restraints weight = 25404.399| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.34 r_work: 0.3576 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9030 Z= 0.116 Angle : 0.682 20.904 12276 Z= 0.375 Chirality : 0.053 0.383 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.349 30.245 1206 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.31 % Favored : 92.13 % Rotamer: Outliers : 1.53 % Allowed : 12.74 % Favored : 85.73 % 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: -1.39 (0.26), residues: 1080 helix: 1.79 (0.29), residues: 366 sheet: -1.76 (0.30), residues: 282 loop : -2.79 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.008 0.001 HIS C 229 PHE 0.015 0.001 PHE B 286 TYR 0.015 0.001 TYR A 139 ARG 0.005 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 400) hydrogen bonds : angle 4.44369 ( 1170) SS BOND : bond 0.00957 ( 12) SS BOND : angle 1.85286 ( 24) covalent geometry : bond 0.00254 ( 9018) covalent geometry : angle 0.67752 (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 133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.377 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: 0.4998 (tt0) cc_final: 0.4735 (mp0) REVERT: A 119 MET cc_start: 0.6501 (mmm) cc_final: 0.6226 (tpp) REVERT: A 394 LEU cc_start: 0.7781 (pp) cc_final: 0.7150 (mt) REVERT: C 111 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6786 (tp40) REVERT: C 129 LYS cc_start: 0.8051 (mttt) cc_final: 0.7832 (mttp) REVERT: C 378 TYR cc_start: 0.8561 (p90) cc_final: 0.8303 (p90) REVERT: C 394 LEU cc_start: 0.7638 (pp) cc_final: 0.7062 (mt) REVERT: B 128 MET cc_start: 0.6470 (mpp) cc_final: 0.6175 (mpp) REVERT: B 150 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 278 GLU cc_start: 0.8141 (tt0) cc_final: 0.7667 (tt0) REVERT: B 394 LEU cc_start: 0.7727 (pp) cc_final: 0.7177 (mt) outliers start: 15 outliers final: 13 residues processed: 124 average time/residue: 0.5986 time to fit residues: 99.5140 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 : 1.478 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 111 GLN 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 299 CYS 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 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145623 restraints weight = 25308.846| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.34 r_work: 0.3552 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.857 9030 Z= 0.436 Angle : 1.185 59.200 12276 Z= 0.656 Chirality : 0.056 0.557 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.343 30.292 1206 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.13 % Favored : 92.31 % Rotamer: Outliers : 1.63 % Allowed : 12.74 % Favored : 85.63 % Cbeta Deviations : 0.10 % 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: -1.38 (0.26), residues: 1080 helix: 1.79 (0.29), residues: 366 sheet: -1.75 (0.30), residues: 282 loop : -2.79 (0.26), residues: 432 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 0.012 0.001 PHE B 286 TYR 0.014 0.001 TYR A 139 ARG 0.003 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 400) hydrogen bonds : angle 4.44261 ( 1170) SS BOND : bond 0.09038 ( 12) SS BOND : angle 12.16650 ( 24) covalent geometry : bond 0.01212 ( 9018) covalent geometry : angle 1.05676 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9270.21 seconds wall clock time: 160 minutes 5.44 seconds (9605.44 seconds total)