Starting phenix.real_space_refine on Sun Aug 24 01:14:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yms_39406/08_2025/8yms_39406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yms_39406/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yms_39406/08_2025/8yms_39406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yms_39406/08_2025/8yms_39406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yms_39406/08_2025/8yms_39406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yms_39406/08_2025/8yms_39406.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5652 2.51 5 N 1482 2.21 5 O 1611 1.98 5 H 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.36, per 1000 atoms: 0.15 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: 0.97 Conformation dependent library (CDL) restraints added in 390.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 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: 0.29 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: 3.42 Time building geometry restraints manager: 1.45 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.090 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.012 0.000 ARG C 290 TYR 0.016 0.001 TYR A 81 PHE 0.024 0.002 PHE A 350 TRP 0.006 0.001 TRP B 54 HIS 0.009 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9018) covalent geometry : angle 0.80683 (12252) SS BOND : bond 0.00376 ( 12) SS BOND : angle 0.82178 ( 24) hydrogen bonds : bond 0.19585 ( 400) hydrogen bonds : angle 8.70705 ( 1170) *********************** 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 : 0.356 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 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: 0.6804 (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: 0.1949 time to fit residues: 34.3098 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.189229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.155517 restraints weight = 24969.839| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.32 r_work: 0.3619 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9030 Z= 0.149 Angle : 0.685 11.779 12276 Z= 0.390 Chirality : 0.054 0.388 1365 Planarity : 0.004 0.044 1581 Dihedral : 5.918 31.817 1206 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.96 % Favored : 91.39 % Rotamer: Outliers : 0.92 % Allowed : 5.81 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.26), residues: 1080 helix: 1.30 (0.29), residues: 369 sheet: -2.03 (0.31), residues: 267 loop : -2.98 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 149 TYR 0.009 0.001 TYR A 170 PHE 0.014 0.001 PHE C 256 TRP 0.008 0.001 TRP A 54 HIS 0.008 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9018) covalent geometry : angle 0.68464 (12252) SS BOND : bond 0.00367 ( 12) SS BOND : angle 0.82897 ( 24) hydrogen bonds : bond 0.04077 ( 400) hydrogen bonds : angle 5.92499 ( 1170) *********************** 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 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.413 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: 0.7960 (mtp) cc_final: 0.7604 (mtt) REVERT: A 394 LEU cc_start: 0.7832 (pp) cc_final: 0.7151 (mt) REVERT: C 254 PHE cc_start: 0.7594 (p90) cc_final: 0.7341 (p90) REVERT: C 342 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6193 (pm20) REVERT: C 394 LEU cc_start: 0.7860 (pp) cc_final: 0.7199 (mt) REVERT: B 262 GLN cc_start: 0.8636 (tt0) cc_final: 0.8420 (tt0) REVERT: B 278 GLU cc_start: 0.8334 (tt0) cc_final: 0.7955 (tt0) REVERT: B 394 LEU cc_start: 0.7742 (pp) cc_final: 0.7094 (mt) outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.2132 time to fit residues: 33.6899 Evaluate side-chains 111 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 13 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.179671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146426 restraints weight = 25511.682| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.31 r_work: 0.3506 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9030 Z= 0.220 Angle : 0.720 11.743 12276 Z= 0.409 Chirality : 0.055 0.395 1365 Planarity : 0.004 0.034 1581 Dihedral : 6.123 33.597 1206 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.44 % Favored : 89.91 % Rotamer: Outliers : 1.53 % Allowed : 9.38 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.25), residues: 1080 helix: 1.22 (0.29), residues: 363 sheet: -2.25 (0.29), residues: 285 loop : -2.88 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 290 TYR 0.011 0.002 TYR A 170 PHE 0.022 0.002 PHE C 256 TRP 0.011 0.001 TRP A 54 HIS 0.010 0.002 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9018) covalent geometry : angle 0.71851 (12252) SS BOND : bond 0.00495 ( 12) SS BOND : angle 1.16319 ( 24) hydrogen bonds : bond 0.03993 ( 400) hydrogen bonds : angle 5.35703 ( 1170) *********************** 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: 15 poor density : 111 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5779 (tt0) cc_final: 0.4830 (mp0) REVERT: A 394 LEU cc_start: 0.7963 (pp) cc_final: 0.7169 (mt) REVERT: C 394 LEU cc_start: 0.7969 (pp) cc_final: 0.7288 (mt) REVERT: B 76 MET cc_start: 0.7998 (mtp) cc_final: 0.7663 (mtt) REVERT: B 262 GLN cc_start: 0.8634 (tt0) cc_final: 0.8417 (tt0) REVERT: B 394 LEU cc_start: 0.7867 (pp) cc_final: 0.7155 (mt) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.2150 time to fit residues: 32.2974 Evaluate side-chains 110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 C residue 67 PHE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 158 SER 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 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN B 55 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.175164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142453 restraints weight = 25572.543| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.29 r_work: 0.3460 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9030 Z= 0.231 Angle : 0.718 11.240 12276 Z= 0.408 Chirality : 0.055 0.388 1365 Planarity : 0.004 0.029 1581 Dihedral : 6.146 34.552 1206 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.26 % Favored : 90.19 % Rotamer: Outliers : 3.16 % Allowed : 9.48 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.25), residues: 1080 helix: 1.13 (0.28), residues: 366 sheet: -2.25 (0.30), residues: 285 loop : -2.92 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 339 TYR 0.013 0.002 TYR C 378 PHE 0.022 0.002 PHE A 110 TRP 0.015 0.002 TRP A 54 HIS 0.007 0.002 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9018) covalent geometry : angle 0.71669 (12252) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.23027 ( 24) hydrogen bonds : bond 0.03821 ( 400) hydrogen bonds : angle 5.13363 ( 1170) *********************** 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 148 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5646 (tt0) cc_final: 0.4820 (mp0) REVERT: A 119 MET cc_start: 0.6523 (mmm) cc_final: 0.6150 (tpp) REVERT: A 394 LEU cc_start: 0.7918 (pp) cc_final: 0.7135 (mt) REVERT: C 394 LEU cc_start: 0.8000 (pp) cc_final: 0.7301 (mt) REVERT: B 128 MET cc_start: 0.6719 (mpp) cc_final: 0.6426 (mpp) REVERT: B 278 GLU cc_start: 0.8282 (tt0) cc_final: 0.7879 (tt0) REVERT: B 394 LEU cc_start: 0.7952 (pp) cc_final: 0.7253 (mt) outliers start: 31 outliers final: 20 residues processed: 134 average time/residue: 0.1894 time to fit residues: 34.0390 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 161 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 175 MET 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 161 GLU 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 161 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** A 264 ASN ** 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 = 0.4048 r_free = 0.4048 target = 0.184370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152774 restraints weight = 24935.164| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.26 r_work: 0.3561 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9030 Z= 0.132 Angle : 0.691 24.379 12276 Z= 0.382 Chirality : 0.053 0.388 1365 Planarity : 0.004 0.030 1581 Dihedral : 5.706 32.738 1206 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 1.73 % Allowed : 11.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.26), residues: 1080 helix: 1.34 (0.28), residues: 375 sheet: -2.06 (0.30), residues: 282 loop : -2.96 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.012 0.001 TYR A 139 PHE 0.016 0.001 PHE C 256 TRP 0.011 0.001 TRP A 54 HIS 0.008 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9018) covalent geometry : angle 0.68721 (12252) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.79957 ( 24) hydrogen bonds : bond 0.03266 ( 400) hydrogen bonds : angle 4.83144 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.334 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 84 GLU cc_start: 0.5339 (tt0) cc_final: 0.4711 (mp0) REVERT: A 119 MET cc_start: 0.6461 (mmm) cc_final: 0.6110 (tpp) REVERT: A 132 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: A 394 LEU cc_start: 0.7834 (pp) cc_final: 0.7176 (mt) REVERT: C 394 LEU cc_start: 0.7840 (pp) cc_final: 0.7215 (mt) REVERT: B 128 MET cc_start: 0.6635 (mpp) cc_final: 0.6345 (mpp) REVERT: B 278 GLU cc_start: 0.8250 (tt0) cc_final: 0.7816 (tt0) REVERT: B 394 LEU cc_start: 0.7835 (pp) cc_final: 0.7219 (mt) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.1945 time to fit residues: 30.9768 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 372 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 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 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 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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** A 264 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.176058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143026 restraints weight = 25481.643| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.37 r_work: 0.3510 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3171 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= 0.148 Angle : 0.678 19.967 12276 Z= 0.378 Chirality : 0.053 0.385 1365 Planarity : 0.004 0.034 1581 Dihedral : 5.573 32.066 1206 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.15 % Favored : 91.30 % Rotamer: Outliers : 2.14 % Allowed : 12.44 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.26), residues: 1080 helix: 1.52 (0.29), residues: 366 sheet: -1.97 (0.30), residues: 282 loop : -2.88 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.013 0.001 TYR B 139 PHE 0.015 0.001 PHE C 256 TRP 0.010 0.001 TRP A 54 HIS 0.006 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9018) covalent geometry : angle 0.67351 (12252) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.86151 ( 24) hydrogen bonds : bond 0.03248 ( 400) hydrogen bonds : angle 4.67371 ( 1170) *********************** 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 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.274 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: 0.5392 (tt0) cc_final: 0.4765 (mp0) REVERT: A 119 MET cc_start: 0.6482 (mmm) cc_final: 0.6150 (tpp) REVERT: A 128 MET cc_start: 0.6415 (ttm) cc_final: 0.6176 (ttt) REVERT: A 132 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: A 394 LEU cc_start: 0.7881 (pp) cc_final: 0.7201 (mt) REVERT: A 409 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4807 (t80) REVERT: C 378 TYR cc_start: 0.8700 (p90) cc_final: 0.8453 (p90) REVERT: C 394 LEU cc_start: 0.7893 (pp) cc_final: 0.7269 (mt) REVERT: B 128 MET cc_start: 0.6614 (mpp) cc_final: 0.6341 (mpp) REVERT: B 150 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7584 (tt) REVERT: B 161 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: B 278 GLU cc_start: 0.8239 (tt0) cc_final: 0.7787 (tt0) REVERT: B 394 LEU cc_start: 0.7853 (pp) cc_final: 0.7238 (mt) outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 0.1867 time to fit residues: 31.8769 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 409 PHE 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 C residue 363 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.179004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145603 restraints weight = 25311.066| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.37 r_work: 0.3541 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9030 Z= 0.126 Angle : 0.650 17.079 12276 Z= 0.364 Chirality : 0.053 0.384 1365 Planarity : 0.003 0.040 1581 Dihedral : 5.402 31.175 1206 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.59 % Favored : 91.85 % Rotamer: Outliers : 2.55 % Allowed : 12.33 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.26), residues: 1080 helix: 1.77 (0.29), residues: 360 sheet: -1.86 (0.30), residues: 282 loop : -2.78 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.014 0.001 TYR B 139 PHE 0.013 0.001 PHE C 256 TRP 0.008 0.001 TRP A 54 HIS 0.006 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9018) covalent geometry : angle 0.64799 (12252) SS BOND : bond 0.00428 ( 12) SS BOND : angle 1.42628 ( 24) hydrogen bonds : bond 0.03096 ( 400) hydrogen bonds : angle 4.55243 ( 1170) *********************** 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 143 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.402 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: 0.5203 (tt0) cc_final: 0.4714 (mp0) REVERT: A 119 MET cc_start: 0.6418 (mmm) cc_final: 0.6083 (tpp) REVERT: A 132 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 394 LEU cc_start: 0.7866 (pp) cc_final: 0.7191 (mt) REVERT: A 409 PHE cc_start: 0.5417 (OUTLIER) cc_final: 0.4840 (t80) REVERT: C 378 TYR cc_start: 0.8625 (p90) cc_final: 0.8397 (p90) REVERT: C 394 LEU cc_start: 0.7833 (pp) cc_final: 0.7239 (mt) REVERT: B 128 MET cc_start: 0.6488 (mpp) cc_final: 0.6195 (mpp) REVERT: B 150 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7577 (tt) REVERT: B 278 GLU cc_start: 0.8179 (tt0) cc_final: 0.7736 (tt0) REVERT: B 394 LEU cc_start: 0.7772 (pp) cc_final: 0.7176 (mt) outliers start: 25 outliers final: 17 residues processed: 132 average time/residue: 0.1856 time to fit residues: 32.4340 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 409 PHE 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 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 158 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.178549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145134 restraints weight = 25359.069| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.38 r_work: 0.3539 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9030 Z= 0.126 Angle : 0.654 15.943 12276 Z= 0.364 Chirality : 0.053 0.383 1365 Planarity : 0.003 0.044 1581 Dihedral : 5.307 30.299 1206 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.59 % Favored : 91.85 % Rotamer: Outliers : 2.65 % Allowed : 12.54 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.26), residues: 1080 helix: 1.85 (0.29), residues: 360 sheet: -1.78 (0.30), residues: 282 loop : -2.74 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.014 0.001 TYR A 139 PHE 0.012 0.001 PHE C 256 TRP 0.008 0.001 TRP A 54 HIS 0.006 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9018) covalent geometry : angle 0.65223 (12252) SS BOND : bond 0.00429 ( 12) SS BOND : angle 1.38077 ( 24) hydrogen bonds : bond 0.03096 ( 400) hydrogen bonds : angle 4.43964 ( 1170) *********************** 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 146 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.418 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: 0.5094 (tt0) cc_final: 0.4693 (mp0) REVERT: A 119 MET cc_start: 0.6400 (mmm) cc_final: 0.6099 (tpp) REVERT: A 128 MET cc_start: 0.6635 (ttm) cc_final: 0.6332 (ttt) REVERT: A 132 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: A 394 LEU cc_start: 0.7849 (pp) cc_final: 0.7183 (mt) REVERT: C 394 LEU cc_start: 0.7789 (pp) cc_final: 0.7228 (mt) REVERT: B 128 MET cc_start: 0.6528 (mpp) cc_final: 0.6222 (mpp) REVERT: B 150 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7552 (tt) REVERT: B 278 GLU cc_start: 0.8176 (tt0) cc_final: 0.7730 (tt0) REVERT: B 394 LEU cc_start: 0.7746 (pp) cc_final: 0.7165 (mt) outliers start: 26 outliers final: 22 residues processed: 133 average time/residue: 0.1934 time to fit residues: 33.9953 Evaluate side-chains 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 132 ASP 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 299 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 408 VAL 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 210 ASP 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 169 SER 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 98 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3941 r_free = 0.3941 target = 0.176417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143408 restraints weight = 25190.525| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.35 r_work: 0.3543 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9030 Z= 0.143 Angle : 0.653 15.259 12276 Z= 0.365 Chirality : 0.053 0.381 1365 Planarity : 0.003 0.046 1581 Dihedral : 5.328 30.165 1206 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.50 % Favored : 91.94 % Rotamer: Outliers : 2.65 % Allowed : 12.84 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.26), residues: 1080 helix: 1.84 (0.29), residues: 363 sheet: -1.75 (0.30), residues: 282 loop : -2.70 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.013 0.001 TYR A 139 PHE 0.014 0.001 PHE C 256 TRP 0.009 0.001 TRP A 54 HIS 0.005 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9018) covalent geometry : angle 0.65082 (12252) SS BOND : bond 0.00455 ( 12) SS BOND : angle 1.33967 ( 24) hydrogen bonds : bond 0.03155 ( 400) hydrogen bonds : angle 4.43643 ( 1170) *********************** 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 141 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.276 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: 0.5120 (tt0) cc_final: 0.4739 (mp0) REVERT: A 119 MET cc_start: 0.6402 (mmm) cc_final: 0.6112 (tpp) REVERT: A 128 MET cc_start: 0.6632 (ttm) cc_final: 0.6367 (ttt) REVERT: A 132 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: A 394 LEU cc_start: 0.7900 (pp) cc_final: 0.7203 (mt) REVERT: C 394 LEU cc_start: 0.7784 (pp) cc_final: 0.7168 (mt) REVERT: B 128 MET cc_start: 0.6578 (mpp) cc_final: 0.6271 (mpp) REVERT: B 150 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7548 (tt) REVERT: B 278 GLU cc_start: 0.8208 (tt0) cc_final: 0.7771 (tt0) REVERT: B 394 LEU cc_start: 0.7790 (pp) cc_final: 0.7182 (mt) outliers start: 26 outliers final: 22 residues processed: 129 average time/residue: 0.1831 time to fit residues: 31.0546 Evaluate side-chains 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 132 ASP 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 299 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 408 VAL 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 210 ASP 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 169 SER Chi-restraints excluded: chain B residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.404 > 50: distance: 161 - 189: 3.050 distance: 222 - 439: 33.508 distance: 253 - 270: 8.211 distance: 270 - 271: 3.252 distance: 270 - 276: 5.500 distance: 271 - 272: 4.120 distance: 271 - 274: 6.366 distance: 271 - 277: 7.282 distance: 272 - 273: 4.889 distance: 272 - 284: 5.108 distance: 274 - 275: 7.409 distance: 275 - 276: 6.430 distance: 276 - 282: 8.761 distance: 276 - 283: 3.635 distance: 284 - 285: 6.700 distance: 284 - 296: 6.115 distance: 285 - 286: 18.330 distance: 285 - 288: 5.883 distance: 285 - 297: 9.974 distance: 286 - 287: 31.410 distance: 286 - 305: 23.451 distance: 288 - 298: 7.677 distance: 288 - 299: 4.848 distance: 291 - 301: 3.003 distance: 292 - 294: 3.200 distance: 294 - 295: 4.504 distance: 295 - 304: 4.243 distance: 305 - 306: 29.890 distance: 305 - 313: 18.320 distance: 306 - 307: 25.725 distance: 306 - 309: 29.484 distance: 306 - 314: 17.462 distance: 307 - 308: 7.945 distance: 307 - 322: 24.413 distance: 309 - 310: 16.674 distance: 309 - 316: 5.778 distance: 310 - 311: 6.074 distance: 310 - 317: 7.295 distance: 310 - 318: 5.927 distance: 311 - 312: 3.286 distance: 312 - 319: 4.703 distance: 312 - 320: 4.802 distance: 312 - 321: 4.567 distance: 322 - 323: 13.223 distance: 322 - 333: 26.592 distance: 323 - 324: 22.661 distance: 323 - 326: 12.407 distance: 323 - 334: 15.512 distance: 324 - 325: 30.600 distance: 324 - 346: 33.690 distance: 326 - 327: 12.158 distance: 326 - 335: 13.620 distance: 326 - 336: 15.240 distance: 327 - 328: 7.071 distance: 327 - 337: 4.312 distance: 327 - 338: 3.610 distance: 328 - 329: 4.827 distance: 331 - 342: 3.095 distance: 346 - 347: 16.041 distance: 346 - 352: 15.911 distance: 347 - 348: 7.122 distance: 347 - 350: 19.018 distance: 347 - 353: 15.755 distance: 348 - 349: 21.877 distance: 348 - 360: 12.060 distance: 350 - 351: 12.422 distance: 350 - 354: 6.850 distance: 350 - 355: 5.338 distance: 351 - 352: 11.918 distance: 351 - 356: 9.276 distance: 351 - 357: 8.731 distance: 352 - 358: 22.636 distance: 352 - 359: 16.470 distance: 360 - 361: 18.828 distance: 360 - 369: 26.362 distance: 361 - 362: 20.114 distance: 361 - 364: 8.778 distance: 361 - 370: 10.381 distance: 362 - 363: 11.062 distance: 362 - 382: 40.401 distance: 364 - 365: 8.466 distance: 364 - 371: 6.010 distance: 364 - 372: 6.914 distance: 365 - 366: 3.277 distance: 365 - 373: 3.529 distance: 382 - 383: 68.404 distance: 382 - 390: 41.034 distance: 383 - 384: 29.318 distance: 383 - 386: 40.146 distance: 383 - 391: 39.399 distance: 384 - 385: 37.436 distance: 384 - 401: 50.405 distance: 386 - 387: 16.928 distance: 386 - 392: 8.858 distance: 386 - 393: 10.957 distance: 387 - 388: 9.110 distance: 387 - 389: 6.390 distance: 387 - 394: 7.202 distance: 388 - 395: 3.338 distance: 388 - 396: 3.204 distance: 401 - 402: 40.205 distance: 401 - 407: 32.816 distance: 402 - 403: 32.923 distance: 402 - 405: 36.902 distance: 402 - 408: 25.926 distance: 403 - 404: 3.448 distance: 403 - 415: 18.806 distance: 405 - 406: 23.323 distance: 405 - 409: 6.181 distance: 405 - 410: 7.237 distance: 406 - 407: 8.712 distance: 406 - 411: 12.105 distance: 406 - 412: 14.859 distance: 407 - 413: 15.435 distance: 407 - 414: 6.665 distance: 415 - 416: 9.805 distance: 415 - 423: 9.960 distance: 416 - 417: 7.796 distance: 416 - 419: 16.613 distance: 416 - 424: 8.040 distance: 417 - 418: 13.505 distance: 417 - 434: 14.642 distance: 419 - 420: 7.690 distance: 419 - 425: 6.300 distance: 419 - 426: 6.604 distance: 420 - 421: 3.205 distance: 420 - 427: 3.451 distance: 434 - 435: 21.996 distance: 434 - 440: 13.597 distance: 435 - 436: 18.187 distance: 435 - 438: 43.650 distance: 435 - 441: 33.280 distance: 436 - 437: 40.099 distance: 436 - 444: 23.717 distance: 438 - 439: 15.456 distance: 438 - 442: 26.179 distance: 438 - 443: 38.219