Starting phenix.real_space_refine on Wed Sep 17 23:17:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymx_39410/09_2025/8ymx_39410.cif" } resolution = 3.27 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= 0.001 sd= 0.024 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 54 5.16 5 C 5232 2.51 5 N 1374 2.21 5 O 1521 1.98 5 H 3957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12138 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 4046 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Restraints were copied for chains: B, C Time building chain proxies: 3.08, per 1000 atoms: 0.25 Number of scatterers: 12138 At special positions: 0 Unit cell: (101.37, 106.95, 96.72, 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 54 16.00 O 1521 8.00 N 1374 7.00 C 5232 6.00 H 3957 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 188 " 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: 0.91 Conformation dependent library (CDL) restraints added in 367.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 35.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.612A pdb=" N LEU A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.747A pdb=" N ASP A 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.546A 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 140 through 146 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.850A pdb=" N ASP A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.502A pdb=" N SER A 237 " --> pdb=" O HIS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.813A pdb=" N ALA A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.703A pdb=" N LYS A 307 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.761A pdb=" N PHE A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 4.206A pdb=" N ARG A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 82 removed outlier: 3.612A pdb=" N LEU B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.747A pdb=" N ASP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.546A 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 140 through 146 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.850A pdb=" N ASP B 217 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.502A pdb=" N SER B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.814A pdb=" N ALA B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.703A pdb=" N LYS B 307 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 315 through 328 removed outlier: 3.760A pdb=" N PHE B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 4.206A pdb=" N ARG B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 82 removed outlier: 3.612A pdb=" N LEU C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.747A pdb=" N ASP C 132 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.546A 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 140 through 146 Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.851A pdb=" N ASP C 217 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.503A pdb=" N SER C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.813A pdb=" N ALA C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.702A pdb=" N LYS C 307 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 308' Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.760A pdb=" N PHE C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.205A pdb=" N ARG C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 393 " --> pdb=" O ASP C 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 removed outlier: 3.776A pdb=" N ARG A 89 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.580A pdb=" N HIS A 179 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 189 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 105 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 103 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 160 Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.777A pdb=" N ARG B 89 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.580A pdb=" N HIS B 179 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 189 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 105 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 103 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160 Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 94 removed outlier: 3.776A pdb=" N ARG C 89 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'C' and resid 179 through 181 removed outlier: 3.579A pdb=" N HIS C 179 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 189 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 105 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 103 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 155 through 160 307 hydrogen bonds defined for protein. 849 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: 2.40 Time building geometry restraints manager: 1.21 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: 3948 1.03 - 1.23: 17 1.23 - 1.42: 3583 1.42 - 1.62: 4707 1.62 - 1.82: 78 Bond restraints: 12333 Sorted by residual: bond pdb=" N PHE C 354 " pdb=" CA PHE C 354 " ideal model delta sigma weight residual 1.462 1.483 -0.022 1.46e-02 4.69e+03 2.20e+00 bond pdb=" N PHE A 354 " pdb=" CA PHE A 354 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.46e-02 4.69e+03 2.13e+00 bond pdb=" N PHE B 354 " pdb=" CA PHE B 354 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.46e-02 4.69e+03 2.12e+00 bond pdb=" C GLN B 212 " pdb=" N PRO B 213 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.27e-02 6.20e+03 1.11e+00 bond pdb=" C GLN C 212 " pdb=" N PRO C 213 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.27e-02 6.20e+03 1.07e+00 ... (remaining 12328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.14: 20286 7.14 - 14.27: 0 14.27 - 21.41: 3 21.41 - 28.55: 9 28.55 - 35.69: 27 Bond angle restraints: 20325 Sorted by residual: angle pdb=" N ILE A 320 " pdb=" CA ILE A 320 " pdb=" HA ILE A 320 " ideal model delta sigma weight residual 110.00 74.31 35.69 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N ILE C 320 " pdb=" CA ILE C 320 " pdb=" HA ILE C 320 " ideal model delta sigma weight residual 110.00 74.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N ILE B 320 " pdb=" CA ILE B 320 " pdb=" HA ILE B 320 " ideal model delta sigma weight residual 110.00 74.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C GLN B 212 " pdb=" CA GLN B 212 " pdb=" HA GLN B 212 " ideal model delta sigma weight residual 109.00 73.51 35.49 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C GLN C 212 " pdb=" CA GLN C 212 " pdb=" HA GLN C 212 " ideal model delta sigma weight residual 109.00 73.53 35.47 3.00e+00 1.11e-01 1.40e+02 ... (remaining 20320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5570 17.81 - 35.63: 653 35.63 - 53.44: 170 53.44 - 71.25: 33 71.25 - 89.06: 24 Dihedral angle restraints: 6450 sinusoidal: 3102 harmonic: 3348 Sorted by residual: dihedral pdb=" CA ARG C 89 " pdb=" C ARG C 89 " pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ARG B 89 " pdb=" C ARG B 89 " pdb=" N ILE B 90 " pdb=" CA ILE B 90 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ARG A 89 " pdb=" C ARG A 89 " pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 1263 0.328 - 0.656: 6 0.656 - 0.985: 0 0.985 - 1.313: 0 1.313 - 1.641: 3 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CB ILE C 320 " pdb=" CA ILE C 320 " pdb=" CG1 ILE C 320 " pdb=" CG2 ILE C 320 " both_signs ideal model delta sigma weight residual False 2.64 1.00 1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" CB ILE A 320 " pdb=" CA ILE A 320 " pdb=" CG1 ILE A 320 " pdb=" CG2 ILE A 320 " both_signs ideal model delta sigma weight residual False 2.64 1.00 1.64 2.00e-01 2.50e+01 6.72e+01 chirality pdb=" CB ILE B 320 " pdb=" CA ILE B 320 " pdb=" CG1 ILE B 320 " pdb=" CG2 ILE B 320 " both_signs ideal model delta sigma weight residual False 2.64 1.01 1.64 2.00e-01 2.50e+01 6.72e+01 ... (remaining 1269 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 212 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C GLN B 212 " 0.076 2.00e-02 2.50e+03 pdb=" O GLN B 212 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 213 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 212 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C GLN C 212 " 0.076 2.00e-02 2.50e+03 pdb=" O GLN C 212 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO C 213 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 212 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLN A 212 " -0.076 2.00e-02 2.50e+03 pdb=" O GLN A 212 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO A 213 " 0.025 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 314 2.13 - 2.75: 15633 2.75 - 3.37: 29468 3.37 - 3.98: 38908 3.98 - 4.60: 59390 Nonbonded interactions: 143713 Sorted by model distance: nonbonded pdb=" OE1 GLU B 161 " pdb=" H ILE B 198 " model vdw 1.516 2.450 nonbonded pdb=" OE1 GLU C 161 " pdb=" H ILE C 198 " model vdw 1.516 2.450 nonbonded pdb=" OE1 GLU A 161 " pdb=" H ILE A 198 " model vdw 1.516 2.450 nonbonded pdb="HH12 ARG A 89 " pdb=" OE2 GLU B 377 " model vdw 1.531 2.450 nonbonded pdb=" HA ILE C 320 " pdb=" HB ILE C 320 " model vdw 1.537 1.952 ... (remaining 143708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.100 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 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 0.040 8379 Z= 0.154 Angle : 0.667 14.950 11382 Z= 0.371 Chirality : 0.094 1.641 1272 Planarity : 0.005 0.045 1473 Dihedral : 17.976 89.065 3093 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 49.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.48 % Favored : 84.23 % Rotamer: Outliers : 0.33 % Allowed : 28.43 % Favored : 71.24 % Cbeta Deviations : 0.31 % 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: -3.38 (0.25), residues: 1008 helix: -0.27 (0.30), residues: 282 sheet: -2.66 (0.36), residues: 192 loop : -3.32 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.012 0.001 TYR C 265 PHE 0.031 0.001 PHE A 397 TRP 0.009 0.002 TRP A 145 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8376) covalent geometry : angle 0.66687 (11376) SS BOND : bond 0.00101 ( 3) SS BOND : angle 1.14522 ( 6) hydrogen bonds : bond 0.12609 ( 307) hydrogen bonds : angle 7.09277 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 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: A 397 PHE cc_start: 0.6399 (m-80) cc_final: 0.6070 (m-80) REVERT: B 397 PHE cc_start: 0.6252 (m-80) cc_final: 0.5940 (m-80) REVERT: C 205 PHE cc_start: 0.7189 (p90) cc_final: 0.6938 (p90) outliers start: 3 outliers final: 1 residues processed: 143 average time/residue: 0.1128 time to fit residues: 24.1746 Evaluate side-chains 138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4632 r_free = 0.4632 target = 0.207583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.184947 restraints weight = 24233.175| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.43 r_work: 0.4287 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8379 Z= 0.197 Angle : 0.636 15.219 11382 Z= 0.341 Chirality : 0.095 1.677 1272 Planarity : 0.005 0.050 1473 Dihedral : 5.261 35.528 1127 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 50.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.38 % Favored : 84.33 % Rotamer: Outliers : 3.49 % Allowed : 24.29 % Favored : 72.22 % Cbeta Deviations : 0.31 % 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: -3.46 (0.25), residues: 1008 helix: -0.32 (0.30), residues: 267 sheet: -2.70 (0.37), residues: 189 loop : -3.30 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 318 TYR 0.010 0.001 TYR B 279 PHE 0.027 0.002 PHE A 397 TRP 0.021 0.006 TRP A 145 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8376) covalent geometry : angle 0.63554 (11376) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.73099 ( 6) hydrogen bonds : bond 0.04005 ( 307) hydrogen bonds : angle 6.38430 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.406 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.2872 (OUTLIER) cc_final: 0.2565 (mtm110) REVERT: B 390 ILE cc_start: 0.7532 (mm) cc_final: 0.7239 (mm) REVERT: B 397 PHE cc_start: 0.6542 (m-80) cc_final: 0.6113 (m-80) REVERT: C 397 PHE cc_start: 0.6502 (m-80) cc_final: 0.6043 (m-80) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.1275 time to fit residues: 32.0263 Evaluate side-chains 171 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4640 r_free = 0.4640 target = 0.208295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.185551 restraints weight = 24422.977| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.45 r_work: 0.4305 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8379 Z= 0.145 Angle : 0.605 15.231 11382 Z= 0.321 Chirality : 0.095 1.665 1272 Planarity : 0.004 0.038 1473 Dihedral : 5.138 37.829 1127 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 48.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.58 % Favored : 84.13 % Rotamer: Outliers : 5.66 % Allowed : 23.64 % Favored : 70.70 % Cbeta Deviations : 0.31 % 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: -3.32 (0.25), residues: 1008 helix: -0.24 (0.31), residues: 267 sheet: -2.32 (0.40), residues: 168 loop : -3.31 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 339 TYR 0.008 0.001 TYR B 279 PHE 0.021 0.001 PHE C 397 TRP 0.016 0.004 TRP B 145 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8376) covalent geometry : angle 0.60444 (11376) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.81247 ( 6) hydrogen bonds : bond 0.03622 ( 307) hydrogen bonds : angle 6.19129 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.367 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: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.4589 (OUTLIER) cc_final: 0.3912 (ptt-90) REVERT: A 145 TRP cc_start: 0.4721 (t-100) cc_final: 0.4418 (t-100) REVERT: A 318 ARG cc_start: 0.2715 (OUTLIER) cc_final: 0.2445 (mtm110) REVERT: A 326 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5588 (t70) REVERT: B 397 PHE cc_start: 0.6548 (m-80) cc_final: 0.6114 (m-80) REVERT: C 278 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: C 397 PHE cc_start: 0.6598 (m-80) cc_final: 0.6079 (m-80) outliers start: 52 outliers final: 35 residues processed: 181 average time/residue: 0.1200 time to fit residues: 32.2423 Evaluate side-chains 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 21 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4644 r_free = 0.4644 target = 0.208661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.186043 restraints weight = 24145.854| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 3.41 r_work: 0.4305 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8379 Z= 0.132 Angle : 0.594 15.262 11382 Z= 0.314 Chirality : 0.095 1.671 1272 Planarity : 0.004 0.039 1473 Dihedral : 5.069 38.800 1127 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 48.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.58 % Favored : 84.13 % Rotamer: Outliers : 5.23 % Allowed : 24.29 % Favored : 70.48 % Cbeta Deviations : 0.31 % 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: -3.27 (0.26), residues: 1008 helix: -0.17 (0.31), residues: 267 sheet: -2.34 (0.40), residues: 180 loop : -3.27 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.008 0.001 TYR B 279 PHE 0.016 0.001 PHE C 397 TRP 0.019 0.004 TRP C 145 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8376) covalent geometry : angle 0.59352 (11376) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.89418 ( 6) hydrogen bonds : bond 0.03432 ( 307) hydrogen bonds : angle 6.06904 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.421 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: symmetry clash REVERT: A 108 ARG cc_start: 0.4571 (OUTLIER) cc_final: 0.3843 (ptt-90) REVERT: A 145 TRP cc_start: 0.4715 (t-100) cc_final: 0.4435 (t-100) REVERT: A 318 ARG cc_start: 0.2747 (OUTLIER) cc_final: 0.2445 (mtm110) REVERT: A 371 TYR cc_start: 0.6981 (m-80) cc_final: 0.6589 (m-80) REVERT: B 108 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.1953 (ptt-90) REVERT: B 397 PHE cc_start: 0.6527 (m-80) cc_final: 0.6163 (m-80) REVERT: C 108 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.1551 (ptt-90) REVERT: C 278 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6484 (tt0) REVERT: C 397 PHE cc_start: 0.6556 (m-80) cc_final: 0.6124 (m-80) outliers start: 48 outliers final: 41 residues processed: 181 average time/residue: 0.1361 time to fit residues: 35.4081 Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 0.0010 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4623 r_free = 0.4623 target = 0.206905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184558 restraints weight = 24244.766| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.38 r_work: 0.4286 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8379 Z= 0.187 Angle : 0.625 15.154 11382 Z= 0.333 Chirality : 0.095 1.668 1272 Planarity : 0.004 0.039 1473 Dihedral : 5.285 39.831 1127 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 52.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.77 % Favored : 83.93 % Rotamer: Outliers : 6.21 % Allowed : 23.86 % Favored : 69.93 % Cbeta Deviations : 0.31 % 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: -3.59 (0.25), residues: 1008 helix: -0.69 (0.29), residues: 282 sheet: -3.05 (0.37), residues: 192 loop : -3.16 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.010 0.001 TYR C 139 PHE 0.017 0.001 PHE A 205 TRP 0.025 0.005 TRP C 145 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8376) covalent geometry : angle 0.62459 (11376) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.98163 ( 6) hydrogen bonds : bond 0.03660 ( 307) hydrogen bonds : angle 6.08391 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 0.374 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 120 VAL cc_start: 0.3305 (t) cc_final: 0.2128 (p) REVERT: A 145 TRP cc_start: 0.4648 (t-100) cc_final: 0.4404 (t-100) REVERT: A 197 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.4021 (mt) REVERT: A 318 ARG cc_start: 0.2737 (OUTLIER) cc_final: 0.2399 (mtm110) REVERT: B 108 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.2108 (ptt-90) REVERT: B 199 TYR cc_start: 0.5100 (t80) cc_final: 0.4859 (t80) REVERT: B 390 ILE cc_start: 0.7375 (mm) cc_final: 0.7154 (mm) REVERT: B 397 PHE cc_start: 0.6624 (m-80) cc_final: 0.6185 (m-80) REVERT: C 108 ARG cc_start: 0.5266 (OUTLIER) cc_final: 0.1716 (ptt-90) REVERT: C 278 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: C 377 GLU cc_start: 0.7517 (tt0) cc_final: 0.7250 (tt0) REVERT: C 397 PHE cc_start: 0.6612 (m-80) cc_final: 0.6294 (m-80) outliers start: 57 outliers final: 40 residues processed: 192 average time/residue: 0.1525 time to fit residues: 40.5887 Evaluate side-chains 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4622 r_free = 0.4622 target = 0.206373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183757 restraints weight = 24317.002| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 3.44 r_work: 0.4280 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8379 Z= 0.179 Angle : 0.619 15.206 11382 Z= 0.329 Chirality : 0.095 1.668 1272 Planarity : 0.004 0.041 1473 Dihedral : 5.319 40.765 1127 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 52.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.58 % Favored : 84.13 % Rotamer: Outliers : 7.08 % Allowed : 22.88 % Favored : 70.04 % Cbeta Deviations : 0.31 % 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: -3.58 (0.25), residues: 1008 helix: -0.68 (0.29), residues: 282 sheet: -2.83 (0.37), residues: 198 loop : -3.26 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.010 0.001 TYR C 139 PHE 0.017 0.001 PHE A 205 TRP 0.021 0.005 TRP C 145 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8376) covalent geometry : angle 0.61858 (11376) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.96993 ( 6) hydrogen bonds : bond 0.03606 ( 307) hydrogen bonds : angle 6.05484 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 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 120 VAL cc_start: 0.3485 (t) cc_final: 0.2245 (p) REVERT: A 145 TRP cc_start: 0.4734 (t-100) cc_final: 0.4515 (t-100) REVERT: A 197 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.4125 (mt) REVERT: A 318 ARG cc_start: 0.2783 (OUTLIER) cc_final: 0.2409 (mtm110) REVERT: B 108 ARG cc_start: 0.5276 (OUTLIER) cc_final: 0.2209 (ptt-90) REVERT: B 199 TYR cc_start: 0.5174 (t80) cc_final: 0.4944 (t80) REVERT: B 390 ILE cc_start: 0.7442 (mm) cc_final: 0.7231 (mm) REVERT: B 397 PHE cc_start: 0.6670 (m-80) cc_final: 0.6188 (m-80) REVERT: C 108 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.1657 (ptt-90) REVERT: C 278 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6507 (tt0) REVERT: C 340 LYS cc_start: 0.4675 (OUTLIER) cc_final: 0.4191 (ptpp) REVERT: C 397 PHE cc_start: 0.6628 (m-80) cc_final: 0.6203 (m-80) outliers start: 65 outliers final: 53 residues processed: 198 average time/residue: 0.1522 time to fit residues: 41.9130 Evaluate side-chains 204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 145 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4621 r_free = 0.4621 target = 0.206361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183968 restraints weight = 24095.526| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.40 r_work: 0.4284 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8379 Z= 0.165 Angle : 0.614 15.085 11382 Z= 0.326 Chirality : 0.095 1.664 1272 Planarity : 0.004 0.060 1473 Dihedral : 5.321 41.531 1127 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 52.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.97 % Favored : 83.73 % Rotamer: Outliers : 7.52 % Allowed : 22.44 % Favored : 70.04 % Cbeta Deviations : 0.31 % 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: -3.53 (0.25), residues: 1008 helix: -0.70 (0.29), residues: 282 sheet: -2.55 (0.39), residues: 177 loop : -3.31 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.010 0.001 TYR B 279 PHE 0.016 0.001 PHE A 205 TRP 0.022 0.005 TRP B 145 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8376) covalent geometry : angle 0.61421 (11376) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.98275 ( 6) hydrogen bonds : bond 0.03539 ( 307) hydrogen bonds : angle 6.04340 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 148 time to evaluate : 0.432 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: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.3482 (t) cc_final: 0.2212 (p) REVERT: A 145 TRP cc_start: 0.4847 (t-100) cc_final: 0.4570 (t-100) REVERT: A 197 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.4110 (mt) REVERT: A 318 ARG cc_start: 0.2788 (OUTLIER) cc_final: 0.2394 (mtm110) REVERT: B 108 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.4671 (mtt90) REVERT: B 397 PHE cc_start: 0.6655 (m-80) cc_final: 0.6163 (m-80) REVERT: C 108 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.1574 (ptt-90) REVERT: C 278 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: C 340 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4126 (ptpp) REVERT: C 397 PHE cc_start: 0.6664 (m-80) cc_final: 0.6213 (m-80) outliers start: 69 outliers final: 57 residues processed: 201 average time/residue: 0.1520 time to fit residues: 42.5230 Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4624 r_free = 0.4624 target = 0.206583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.184028 restraints weight = 23979.072| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 3.42 r_work: 0.4293 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8379 Z= 0.144 Angle : 0.605 15.055 11382 Z= 0.320 Chirality : 0.094 1.661 1272 Planarity : 0.004 0.039 1473 Dihedral : 5.232 41.874 1127 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 50.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.58 % Favored : 84.13 % Rotamer: Outliers : 6.86 % Allowed : 23.31 % Favored : 69.83 % Cbeta Deviations : 0.31 % 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: -3.42 (0.26), residues: 1008 helix: -0.35 (0.31), residues: 267 sheet: -2.45 (0.39), residues: 180 loop : -3.33 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 89 TYR 0.009 0.001 TYR C 139 PHE 0.014 0.001 PHE A 205 TRP 0.024 0.005 TRP C 145 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8376) covalent geometry : angle 0.60484 (11376) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.99617 ( 6) hydrogen bonds : bond 0.03395 ( 307) hydrogen bonds : angle 6.01451 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.374 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 120 VAL cc_start: 0.3469 (t) cc_final: 0.2200 (p) REVERT: A 145 TRP cc_start: 0.4812 (t-100) cc_final: 0.4536 (t-100) REVERT: A 206 VAL cc_start: 0.7563 (p) cc_final: 0.7311 (t) REVERT: A 318 ARG cc_start: 0.2770 (OUTLIER) cc_final: 0.2376 (mtm110) REVERT: A 397 PHE cc_start: 0.6560 (m-10) cc_final: 0.6218 (m-10) REVERT: B 108 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.4550 (mtt90) REVERT: B 397 PHE cc_start: 0.6677 (m-80) cc_final: 0.6170 (m-80) REVERT: C 108 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.1469 (ptt-90) REVERT: C 120 VAL cc_start: 0.3234 (t) cc_final: 0.1819 (p) REVERT: C 241 THR cc_start: 0.4406 (m) cc_final: 0.4052 (m) REVERT: C 278 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6500 (tt0) REVERT: C 397 PHE cc_start: 0.6677 (m-80) cc_final: 0.6216 (m-80) outliers start: 63 outliers final: 52 residues processed: 198 average time/residue: 0.1413 time to fit residues: 39.8422 Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4630 r_free = 0.4630 target = 0.207595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.185302 restraints weight = 23956.557| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 3.40 r_work: 0.4293 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8379 Z= 0.157 Angle : 0.613 15.170 11382 Z= 0.323 Chirality : 0.095 1.666 1272 Planarity : 0.004 0.036 1473 Dihedral : 5.268 42.171 1127 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 52.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 16.37 % Favored : 83.33 % Rotamer: Outliers : 6.97 % Allowed : 23.42 % Favored : 69.61 % Cbeta Deviations : 0.31 % 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: -3.45 (0.26), residues: 1008 helix: -0.37 (0.31), residues: 267 sheet: -2.46 (0.39), residues: 180 loop : -3.36 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 89 TYR 0.010 0.001 TYR C 139 PHE 0.015 0.001 PHE A 205 TRP 0.032 0.006 TRP C 145 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8376) covalent geometry : angle 0.61240 (11376) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.98943 ( 6) hydrogen bonds : bond 0.03430 ( 307) hydrogen bonds : angle 5.99153 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 0.377 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: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.3456 (t) cc_final: 0.2134 (p) REVERT: A 145 TRP cc_start: 0.4750 (t-100) cc_final: 0.4489 (t-100) REVERT: A 197 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.4167 (mt) REVERT: A 318 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.2469 (mtm110) REVERT: A 397 PHE cc_start: 0.6550 (m-10) cc_final: 0.6174 (m-10) REVERT: B 108 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4708 (mtt90) REVERT: B 120 VAL cc_start: 0.2858 (t) cc_final: 0.1494 (p) REVERT: B 397 PHE cc_start: 0.6727 (m-80) cc_final: 0.6248 (m-80) REVERT: C 108 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.1528 (ptt-90) REVERT: C 120 VAL cc_start: 0.3273 (t) cc_final: 0.1824 (p) REVERT: C 241 THR cc_start: 0.4474 (m) cc_final: 0.4121 (m) REVERT: C 340 LYS cc_start: 0.4636 (OUTLIER) cc_final: 0.4102 (ptpp) REVERT: C 397 PHE cc_start: 0.6665 (m-80) cc_final: 0.6193 (m-80) outliers start: 64 outliers final: 56 residues processed: 202 average time/residue: 0.1509 time to fit residues: 42.2385 Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4618 r_free = 0.4618 target = 0.206143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.183539 restraints weight = 24050.699| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.42 r_work: 0.4284 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8379 Z= 0.167 Angle : 0.621 15.062 11382 Z= 0.328 Chirality : 0.094 1.661 1272 Planarity : 0.004 0.064 1473 Dihedral : 5.319 42.709 1127 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 52.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.87 % Favored : 83.83 % Rotamer: Outliers : 6.86 % Allowed : 23.42 % Favored : 69.72 % Cbeta Deviations : 0.31 % 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: -3.48 (0.26), residues: 1008 helix: -0.41 (0.31), residues: 267 sheet: -2.48 (0.38), residues: 180 loop : -3.37 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.010 0.001 TYR B 265 PHE 0.016 0.001 PHE A 205 TRP 0.037 0.006 TRP C 145 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8376) covalent geometry : angle 0.62074 (11376) SS BOND : bond 0.00280 ( 3) SS BOND : angle 1.00488 ( 6) hydrogen bonds : bond 0.03462 ( 307) hydrogen bonds : angle 5.98643 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 0.374 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: symmetry clash REVERT: A 120 VAL cc_start: 0.3435 (t) cc_final: 0.2113 (p) REVERT: A 145 TRP cc_start: 0.4809 (t-100) cc_final: 0.4529 (t-100) REVERT: A 197 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4190 (mt) REVERT: A 318 ARG cc_start: 0.2887 (OUTLIER) cc_final: 0.2456 (mtm110) REVERT: B 108 ARG cc_start: 0.5242 (OUTLIER) cc_final: 0.4759 (mtt90) REVERT: B 397 PHE cc_start: 0.6709 (m-80) cc_final: 0.6211 (m-80) REVERT: C 108 ARG cc_start: 0.5128 (OUTLIER) cc_final: 0.1539 (ptt-90) REVERT: C 120 VAL cc_start: 0.3185 (t) cc_final: 0.1710 (p) REVERT: C 241 THR cc_start: 0.4452 (m) cc_final: 0.4109 (m) REVERT: C 340 LYS cc_start: 0.4686 (OUTLIER) cc_final: 0.4266 (ptpp) REVERT: C 397 PHE cc_start: 0.6727 (m-80) cc_final: 0.6250 (m-80) outliers start: 63 outliers final: 56 residues processed: 200 average time/residue: 0.1534 time to fit residues: 42.5418 Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 373 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 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 = 0.4605 r_free = 0.4605 target = 0.205133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.183060 restraints weight = 23996.324| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 3.37 r_work: 0.4264 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8379 Z= 0.229 Angle : 0.665 15.091 11382 Z= 0.355 Chirality : 0.095 1.656 1272 Planarity : 0.004 0.053 1473 Dihedral : 5.674 44.162 1127 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 57.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 17.16 % Favored : 82.54 % Rotamer: Outliers : 6.64 % Allowed : 23.86 % Favored : 69.50 % Cbeta Deviations : 0.31 % 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: -3.75 (0.25), residues: 1008 helix: -0.95 (0.29), residues: 282 sheet: -2.68 (0.38), residues: 177 loop : -3.40 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 89 TYR 0.010 0.001 TYR C 139 PHE 0.016 0.002 PHE A 205 TRP 0.047 0.008 TRP C 145 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8376) covalent geometry : angle 0.66495 (11376) SS BOND : bond 0.00343 ( 3) SS BOND : angle 1.06856 ( 6) hydrogen bonds : bond 0.03791 ( 307) hydrogen bonds : angle 6.12397 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.85 seconds wall clock time: 51 minutes 49.46 seconds (3109.46 seconds total)