Starting phenix.real_space_refine on Sat Aug 23 00:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpf_18549/08_2025/8qpf_18549.cif" } resolution = 2.53 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= 0.026 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5850 2.51 5 N 1434 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "C" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Time building chain proxies: 2.49, per 1000 atoms: 0.27 Number of scatterers: 9085 At special positions: 0 Unit cell: (87.36, 94.08, 80.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1744 8.00 N 1434 7.00 C 5850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.71 Conformation dependent library (CDL) restraints added in 290.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 78.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.511A pdb=" N ASN A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 59 removed outlier: 4.054A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 87 through 110 removed outlier: 4.010A pdb=" N GLY A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 203 through 226 removed outlier: 3.570A pdb=" N GLY A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.557A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 280 removed outlier: 3.750A pdb=" N PHE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.215A pdb=" N ALA A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 348 through 382 removed outlier: 3.532A pdb=" N PHE A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Proline residue: A 371 - end of helix removed outlier: 3.711A pdb=" N VAL A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 395 through 398 removed outlier: 3.931A pdb=" N GLY A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'B' and resid 3 through 32 removed outlier: 3.550A pdb=" N ASN B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.012A pdb=" N PHE B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 87 through 108 removed outlier: 3.636A pdb=" N ALA B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 203 through 226 removed outlier: 3.558A pdb=" N GLY B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 256 removed outlier: 3.545A pdb=" N VAL B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 3.686A pdb=" N PHE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 311 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 323 through 338 removed outlier: 4.211A pdb=" N ALA B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 348 through 382 removed outlier: 3.533A pdb=" N PHE B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Proline residue: B 371 - end of helix removed outlier: 3.666A pdb=" N VAL B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 395 through 398 removed outlier: 3.967A pdb=" N GLY B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'C' and resid 3 through 32 removed outlier: 3.547A pdb=" N ASN C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 59 removed outlier: 4.001A pdb=" N PHE C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 66 Processing helix chain 'C' and resid 87 through 110 removed outlier: 3.981A pdb=" N GLY C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 203 through 226 removed outlier: 3.505A pdb=" N GLY C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 256 removed outlier: 3.567A pdb=" N VAL C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 3.738A pdb=" N PHE C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 311 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 323 through 338 removed outlier: 4.200A pdb=" N ALA C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 348 through 382 removed outlier: 3.516A pdb=" N PHE C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 370 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix removed outlier: 3.628A pdb=" N VAL C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 395 through 398 removed outlier: 3.975A pdb=" N GLY C 398 " --> pdb=" O LEU C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 395 through 398' Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 191 removed outlier: 3.515A pdb=" N GLY B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 653 hydrogen bonds defined for protein. 1935 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: 1.78 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2735 1.35 - 1.47: 2435 1.47 - 1.59: 3851 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 9099 Sorted by residual: bond pdb=" CB TRP B 218 " pdb=" CG TRP B 218 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.43e+00 bond pdb=" CB TRP A 218 " pdb=" CG TRP A 218 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.17e+00 bond pdb=" CB TRP C 218 " pdb=" CG TRP C 218 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.64e+00 bond pdb=" CG LEU B 216 " pdb=" CD2 LEU B 216 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 bond pdb=" CG LEU A 216 " pdb=" CD2 LEU A 216 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 12270 3.47 - 6.95: 81 6.95 - 10.42: 19 10.42 - 13.89: 0 13.89 - 17.36: 2 Bond angle restraints: 12372 Sorted by residual: angle pdb=" CB MET A 97 " pdb=" CG MET A 97 " pdb=" SD MET A 97 " ideal model delta sigma weight residual 112.70 130.06 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" CB MET C 97 " pdb=" CG MET C 97 " pdb=" SD MET C 97 " ideal model delta sigma weight residual 112.70 127.04 -14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C CYS B 255 " pdb=" N ILE B 256 " pdb=" CA ILE B 256 " ideal model delta sigma weight residual 121.97 129.84 -7.87 1.80e+00 3.09e-01 1.91e+01 angle pdb=" C CYS A 255 " pdb=" N ILE A 256 " pdb=" CA ILE A 256 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C CYS C 255 " pdb=" N ILE C 256 " pdb=" CA ILE C 256 " ideal model delta sigma weight residual 121.97 129.80 -7.83 1.80e+00 3.09e-01 1.89e+01 ... (remaining 12367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4515 17.18 - 34.36: 453 34.36 - 51.54: 103 51.54 - 68.72: 20 68.72 - 85.90: 6 Dihedral angle restraints: 5097 sinusoidal: 1842 harmonic: 3255 Sorted by residual: dihedral pdb=" CA THR A 104 " pdb=" C THR A 104 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" N ILE C 105 " pdb=" CA ILE C 105 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR B 104 " pdb=" C THR B 104 " pdb=" N ILE B 105 " pdb=" CA ILE B 105 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1269 0.072 - 0.144: 153 0.144 - 0.215: 15 0.215 - 0.287: 0 0.287 - 0.359: 3 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB ILE C 256 " pdb=" CA ILE C 256 " pdb=" CG1 ILE C 256 " pdb=" CG2 ILE C 256 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 256 " pdb=" CA ILE B 256 " pdb=" CG1 ILE B 256 " pdb=" CG2 ILE B 256 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE A 256 " pdb=" CA ILE A 256 " pdb=" CG1 ILE A 256 " pdb=" CG2 ILE A 256 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1437 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 205 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 204 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 205 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 205 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.031 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2211 2.79 - 3.31: 8642 3.31 - 3.84: 17312 3.84 - 4.37: 20634 4.37 - 4.90: 34349 Nonbonded interactions: 83148 Sorted by model distance: nonbonded pdb=" OG SER A 234 " pdb=" OG SER B 90 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 204 " pdb=" OG1 THR B 207 " model vdw 2.289 3.040 nonbonded pdb=" O LEU A 204 " pdb=" OG1 THR A 207 " model vdw 2.311 3.040 nonbonded pdb=" NE1 TRP C 218 " pdb=" OG1 THR C 279 " model vdw 2.316 3.120 nonbonded pdb=" O PHE B 79 " pdb=" O HOH B 701 " model vdw 2.334 3.040 ... (remaining 83143 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: 0.650 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.005 0.079 9099 Z= 0.256 Angle : 0.838 17.365 12372 Z= 0.464 Chirality : 0.049 0.359 1440 Planarity : 0.007 0.072 1533 Dihedral : 14.754 85.903 3033 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.25 % Favored : 97.49 % Rotamer: Outliers : 0.75 % Allowed : 13.95 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.22), residues: 1155 helix: 0.25 (0.16), residues: 837 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 376 TYR 0.026 0.003 TYR C 119 PHE 0.020 0.002 PHE B 221 TRP 0.015 0.002 TRP B 218 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9099) covalent geometry : angle 0.83763 (12372) hydrogen bonds : bond 0.12619 ( 653) hydrogen bonds : angle 6.85838 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.353 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 174 average time/residue: 0.6361 time to fit residues: 117.7262 Evaluate side-chains 123 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 231 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 95 GLN A 259 GLN B 22 GLN B 259 GLN C 197 ASN C 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.090526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.071769 restraints weight = 16493.788| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.00 r_work: 0.2620 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9099 Z= 0.148 Angle : 0.547 8.788 12372 Z= 0.295 Chirality : 0.039 0.209 1440 Planarity : 0.004 0.039 1533 Dihedral : 4.622 25.027 1235 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.24), residues: 1155 helix: 1.69 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 376 TYR 0.025 0.002 TYR A 119 PHE 0.019 0.001 PHE C 221 TRP 0.013 0.001 TRP B 257 HIS 0.004 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9099) covalent geometry : angle 0.54666 (12372) hydrogen bonds : bond 0.05171 ( 653) hydrogen bonds : angle 5.08905 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8557 (m-30) cc_final: 0.8320 (m-30) REVERT: A 339 ASP cc_start: 0.8142 (t0) cc_final: 0.7880 (t0) REVERT: B 339 ASP cc_start: 0.8159 (t0) cc_final: 0.7865 (t0) REVERT: C 161 ASP cc_start: 0.9177 (t70) cc_final: 0.8965 (t70) REVERT: C 259 GLN cc_start: 0.8134 (pt0) cc_final: 0.7843 (pp30) REVERT: C 339 ASP cc_start: 0.8066 (t0) cc_final: 0.7536 (t0) outliers start: 18 outliers final: 9 residues processed: 147 average time/residue: 0.6127 time to fit residues: 96.0127 Evaluate side-chains 132 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 45 ASN B 22 GLN C 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.074169 restraints weight = 16439.704| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.99 r_work: 0.2642 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9099 Z= 0.129 Angle : 0.508 7.137 12372 Z= 0.276 Chirality : 0.038 0.182 1440 Planarity : 0.003 0.034 1533 Dihedral : 4.185 14.917 1227 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Rotamer: Outliers : 1.92 % Allowed : 17.15 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.25), residues: 1155 helix: 2.32 (0.17), residues: 843 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 376 TYR 0.024 0.001 TYR B 119 PHE 0.014 0.001 PHE A 221 TRP 0.018 0.001 TRP A 257 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9099) covalent geometry : angle 0.50809 (12372) hydrogen bonds : bond 0.04717 ( 653) hydrogen bonds : angle 4.81058 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.360 Fit side-chains REVERT: A 112 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9309 (mt-10) REVERT: A 156 GLN cc_start: 0.9025 (tt0) cc_final: 0.8562 (tm-30) REVERT: A 259 GLN cc_start: 0.8166 (pt0) cc_final: 0.7381 (pp30) REVERT: A 339 ASP cc_start: 0.8112 (t0) cc_final: 0.7795 (t0) REVERT: B 259 GLN cc_start: 0.8096 (pt0) cc_final: 0.7406 (pp30) REVERT: B 339 ASP cc_start: 0.8204 (t0) cc_final: 0.7872 (t0) REVERT: C 259 GLN cc_start: 0.8203 (pt0) cc_final: 0.7917 (pp30) REVERT: C 339 ASP cc_start: 0.8154 (t0) cc_final: 0.7618 (t0) REVERT: C 341 GLN cc_start: 0.8817 (pp30) cc_final: 0.8593 (pt0) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 0.5964 time to fit residues: 95.1341 Evaluate side-chains 140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 191 ASN A 197 ASN B 323 HIS C 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.085992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.067084 restraints weight = 17047.648| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.03 r_work: 0.2547 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9099 Z= 0.189 Angle : 0.546 7.406 12372 Z= 0.292 Chirality : 0.040 0.180 1440 Planarity : 0.003 0.030 1533 Dihedral : 4.086 15.104 1227 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.08 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 17.36 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.25), residues: 1155 helix: 2.59 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.022 0.002 TYR C 119 PHE 0.026 0.001 PHE B 221 TRP 0.020 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9099) covalent geometry : angle 0.54599 (12372) hydrogen bonds : bond 0.05357 ( 653) hydrogen bonds : angle 4.82606 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.245 Fit side-chains REVERT: A 156 GLN cc_start: 0.9063 (tt0) cc_final: 0.8619 (tm-30) REVERT: A 339 ASP cc_start: 0.8175 (t0) cc_final: 0.7835 (t0) REVERT: B 156 GLN cc_start: 0.9115 (tt0) cc_final: 0.8678 (tm-30) REVERT: B 259 GLN cc_start: 0.8127 (pt0) cc_final: 0.7449 (pp30) REVERT: B 339 ASP cc_start: 0.8273 (t0) cc_final: 0.7921 (t0) REVERT: C 218 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.7586 (t-100) REVERT: C 259 GLN cc_start: 0.8284 (pt0) cc_final: 0.8005 (pp30) REVERT: C 339 ASP cc_start: 0.8220 (t0) cc_final: 0.7654 (t0) REVERT: C 341 GLN cc_start: 0.8870 (pp30) cc_final: 0.8562 (pt0) outliers start: 18 outliers final: 12 residues processed: 139 average time/residue: 0.6459 time to fit residues: 95.6121 Evaluate side-chains 129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 278 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN C 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.073560 restraints weight = 16691.563| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.99 r_work: 0.2638 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9099 Z= 0.121 Angle : 0.510 7.365 12372 Z= 0.272 Chirality : 0.038 0.180 1440 Planarity : 0.003 0.030 1533 Dihedral : 4.050 16.457 1227 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.51 % Favored : 97.23 % Rotamer: Outliers : 2.13 % Allowed : 17.89 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.25), residues: 1155 helix: 2.83 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.18 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.028 0.002 TYR B 119 PHE 0.022 0.001 PHE A 221 TRP 0.016 0.001 TRP C 257 HIS 0.002 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9099) covalent geometry : angle 0.50982 (12372) hydrogen bonds : bond 0.04515 ( 653) hydrogen bonds : angle 4.56636 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9202 (mt-10) REVERT: A 156 GLN cc_start: 0.9064 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 259 GLN cc_start: 0.8278 (pt0) cc_final: 0.7499 (pp30) REVERT: A 339 ASP cc_start: 0.8136 (t0) cc_final: 0.7797 (t0) REVERT: A 399 GLU cc_start: 0.5252 (pm20) cc_final: 0.4917 (pt0) REVERT: B 156 GLN cc_start: 0.9110 (tt0) cc_final: 0.8669 (tm-30) REVERT: B 161 ASP cc_start: 0.8990 (t70) cc_final: 0.8645 (t0) REVERT: B 339 ASP cc_start: 0.8200 (t0) cc_final: 0.7842 (t0) REVERT: C 221 PHE cc_start: 0.8372 (t80) cc_final: 0.8148 (t80) REVERT: C 259 GLN cc_start: 0.8322 (pt0) cc_final: 0.8029 (pp30) REVERT: C 339 ASP cc_start: 0.8190 (t0) cc_final: 0.7604 (t0) REVERT: C 341 GLN cc_start: 0.8930 (pp30) cc_final: 0.8641 (pt0) outliers start: 20 outliers final: 11 residues processed: 143 average time/residue: 0.6012 time to fit residues: 91.8339 Evaluate side-chains 131 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.072278 restraints weight = 16711.790| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.00 r_work: 0.2622 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9099 Z= 0.128 Angle : 0.514 8.300 12372 Z= 0.275 Chirality : 0.038 0.185 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.966 15.587 1227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 19.70 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.25), residues: 1155 helix: 2.89 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.022 0.002 TYR C 119 PHE 0.020 0.001 PHE A 221 TRP 0.014 0.001 TRP C 257 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9099) covalent geometry : angle 0.51423 (12372) hydrogen bonds : bond 0.04629 ( 653) hydrogen bonds : angle 4.54641 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9265 (mt-10) REVERT: A 156 GLN cc_start: 0.9083 (tt0) cc_final: 0.8598 (tm-30) REVERT: A 258 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7498 (mm-40) REVERT: A 259 GLN cc_start: 0.8356 (pt0) cc_final: 0.7645 (pp30) REVERT: A 339 ASP cc_start: 0.8185 (t0) cc_final: 0.7839 (t0) REVERT: A 399 GLU cc_start: 0.5240 (pm20) cc_final: 0.4906 (pt0) REVERT: B 156 GLN cc_start: 0.9120 (tt0) cc_final: 0.8669 (tm-30) REVERT: B 161 ASP cc_start: 0.9017 (t70) cc_final: 0.8701 (t0) REVERT: B 339 ASP cc_start: 0.8221 (t0) cc_final: 0.7858 (t0) REVERT: B 399 GLU cc_start: 0.3832 (OUTLIER) cc_final: 0.3575 (pt0) REVERT: C 218 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.7760 (t-100) REVERT: C 259 GLN cc_start: 0.8366 (pt0) cc_final: 0.8067 (pp30) REVERT: C 339 ASP cc_start: 0.8214 (t0) cc_final: 0.7623 (t0) REVERT: C 341 GLN cc_start: 0.8962 (pp30) cc_final: 0.8640 (pt0) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 0.6332 time to fit residues: 93.0748 Evaluate side-chains 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.0370 chunk 40 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.085031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.066166 restraints weight = 17243.245| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.04 r_work: 0.2526 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9099 Z= 0.204 Angle : 0.564 9.014 12372 Z= 0.303 Chirality : 0.040 0.180 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.990 16.102 1227 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.25 % Favored : 97.49 % Rotamer: Outliers : 2.24 % Allowed : 19.17 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.25), residues: 1155 helix: 2.78 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.031 0.002 TYR B 119 PHE 0.026 0.001 PHE A 221 TRP 0.015 0.001 TRP C 257 HIS 0.002 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9099) covalent geometry : angle 0.56397 (12372) hydrogen bonds : bond 0.05491 ( 653) hydrogen bonds : angle 4.72986 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.394 Fit side-chains REVERT: A 156 GLN cc_start: 0.9073 (tt0) cc_final: 0.8626 (tm-30) REVERT: A 259 GLN cc_start: 0.8204 (pt0) cc_final: 0.7527 (pp30) REVERT: A 339 ASP cc_start: 0.8212 (t0) cc_final: 0.7854 (t0) REVERT: B 80 TYR cc_start: 0.6045 (t80) cc_final: 0.5826 (t80) REVERT: B 156 GLN cc_start: 0.9120 (tt0) cc_final: 0.8665 (tm-30) REVERT: B 161 ASP cc_start: 0.9040 (t70) cc_final: 0.8739 (t0) REVERT: B 259 GLN cc_start: 0.8356 (pt0) cc_final: 0.7664 (pp30) REVERT: B 339 ASP cc_start: 0.8376 (t0) cc_final: 0.8020 (t0) REVERT: C 218 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.7058 (t-100) REVERT: C 259 GLN cc_start: 0.8396 (pt0) cc_final: 0.8148 (pp30) REVERT: C 339 ASP cc_start: 0.8307 (t0) cc_final: 0.7725 (t0) REVERT: C 341 GLN cc_start: 0.8984 (pp30) cc_final: 0.8661 (pt0) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.6534 time to fit residues: 94.6083 Evaluate side-chains 128 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 100 optimal weight: 0.0870 chunk 23 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.091736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.073176 restraints weight = 16742.114| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.97 r_work: 0.2642 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9099 Z= 0.120 Angle : 0.521 9.172 12372 Z= 0.279 Chirality : 0.038 0.193 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.992 15.700 1227 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.60 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 19.81 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.25), residues: 1155 helix: 2.94 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.022 0.001 TYR A 119 PHE 0.023 0.001 PHE B 221 TRP 0.013 0.001 TRP C 257 HIS 0.003 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9099) covalent geometry : angle 0.52148 (12372) hydrogen bonds : bond 0.04428 ( 653) hydrogen bonds : angle 4.46869 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8986 (mt-10) REVERT: A 156 GLN cc_start: 0.9063 (tt0) cc_final: 0.8568 (tm-30) REVERT: A 259 GLN cc_start: 0.8422 (pt0) cc_final: 0.7688 (pp30) REVERT: A 339 ASP cc_start: 0.8183 (t0) cc_final: 0.7833 (t0) REVERT: B 112 GLU cc_start: 0.9312 (mt-10) cc_final: 0.9108 (mt-10) REVERT: B 156 GLN cc_start: 0.9123 (tt0) cc_final: 0.8643 (tm-30) REVERT: B 161 ASP cc_start: 0.8959 (t70) cc_final: 0.8713 (t0) REVERT: B 339 ASP cc_start: 0.8245 (t0) cc_final: 0.7888 (t0) REVERT: C 221 PHE cc_start: 0.8437 (t80) cc_final: 0.8204 (t80) REVERT: C 259 GLN cc_start: 0.8367 (pt0) cc_final: 0.7799 (pp30) REVERT: C 339 ASP cc_start: 0.8280 (t0) cc_final: 0.7652 (t0) REVERT: C 341 GLN cc_start: 0.9033 (pp30) cc_final: 0.8684 (pt0) outliers start: 15 outliers final: 11 residues processed: 146 average time/residue: 0.5985 time to fit residues: 93.5242 Evaluate side-chains 138 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.089928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.071083 restraints weight = 16832.295| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.02 r_work: 0.2611 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9099 Z= 0.143 Angle : 0.559 10.939 12372 Z= 0.292 Chirality : 0.039 0.203 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.934 16.326 1227 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.08 % Favored : 97.66 % Rotamer: Outliers : 1.60 % Allowed : 19.91 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.25), residues: 1155 helix: 2.93 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.028 0.002 TYR B 119 PHE 0.022 0.001 PHE B 221 TRP 0.013 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9099) covalent geometry : angle 0.55868 (12372) hydrogen bonds : bond 0.04730 ( 653) hydrogen bonds : angle 4.53825 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.9052 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 259 GLN cc_start: 0.8437 (pt0) cc_final: 0.7723 (pp30) REVERT: A 339 ASP cc_start: 0.8181 (t0) cc_final: 0.7805 (t0) REVERT: B 156 GLN cc_start: 0.9122 (tt0) cc_final: 0.8635 (tm-30) REVERT: B 161 ASP cc_start: 0.8952 (t70) cc_final: 0.8705 (t0) REVERT: B 339 ASP cc_start: 0.8296 (t0) cc_final: 0.7929 (t0) REVERT: C 221 PHE cc_start: 0.8491 (t80) cc_final: 0.8291 (t80) REVERT: C 259 GLN cc_start: 0.8377 (pt0) cc_final: 0.7804 (pp30) REVERT: C 339 ASP cc_start: 0.8283 (t0) cc_final: 0.7666 (t0) REVERT: C 341 GLN cc_start: 0.9011 (pp30) cc_final: 0.8645 (pp30) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.5702 time to fit residues: 83.6468 Evaluate side-chains 132 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.073739 restraints weight = 16725.043| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.98 r_work: 0.2650 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9099 Z= 0.125 Angle : 0.554 12.329 12372 Z= 0.290 Chirality : 0.038 0.206 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.910 15.062 1227 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Rotamer: Outliers : 1.38 % Allowed : 20.55 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.25), residues: 1155 helix: 2.96 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.023 0.002 TYR A 119 PHE 0.023 0.001 PHE A 221 TRP 0.013 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9099) covalent geometry : angle 0.55392 (12372) hydrogen bonds : bond 0.04400 ( 653) hydrogen bonds : angle 4.44055 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.241 Fit side-chains REVERT: A 112 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9091 (mt-10) REVERT: A 156 GLN cc_start: 0.9088 (tt0) cc_final: 0.8590 (tm-30) REVERT: A 202 ASP cc_start: 0.8540 (m-30) cc_final: 0.8315 (m-30) REVERT: A 259 GLN cc_start: 0.8458 (pt0) cc_final: 0.7744 (pp30) REVERT: A 339 ASP cc_start: 0.8246 (t0) cc_final: 0.7895 (t0) REVERT: B 156 GLN cc_start: 0.9146 (tt0) cc_final: 0.8653 (tm-30) REVERT: B 161 ASP cc_start: 0.8905 (t70) cc_final: 0.8673 (t0) REVERT: B 259 GLN cc_start: 0.8424 (pt0) cc_final: 0.7800 (pp30) REVERT: B 339 ASP cc_start: 0.8317 (t0) cc_final: 0.7929 (t0) REVERT: C 259 GLN cc_start: 0.8404 (pt0) cc_final: 0.7861 (pp30) REVERT: C 339 ASP cc_start: 0.8302 (t0) cc_final: 0.7682 (t0) REVERT: C 341 GLN cc_start: 0.9066 (pp30) cc_final: 0.8699 (pp30) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 0.4702 time to fit residues: 70.8145 Evaluate side-chains 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.076710 restraints weight = 16589.648| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.78 r_work: 0.2744 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9099 Z= 0.131 Angle : 0.552 13.243 12372 Z= 0.290 Chirality : 0.039 0.207 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.909 16.063 1227 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.16 % Favored : 97.58 % Rotamer: Outliers : 1.06 % Allowed : 21.09 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.25), residues: 1155 helix: 2.98 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.029 0.002 TYR B 119 PHE 0.024 0.001 PHE A 221 TRP 0.013 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9099) covalent geometry : angle 0.55214 (12372) hydrogen bonds : bond 0.04487 ( 653) hydrogen bonds : angle 4.43867 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.27 seconds wall clock time: 50 minutes 54.87 seconds (3054.87 seconds total)