Starting phenix.real_space_refine on Thu Feb 13 09:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpf_18549/02_2025/8qpf_18549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpf_18549/02_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_18549/02_2025/8qpf_18549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpf_18549/02_2025/8qpf_18549.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpf_18549/02_2025/8qpf_18549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpf_18549/02_2025/8qpf_18549.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.30, per 1000 atoms: 0.58 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: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.75 Time building geometry restraints manager: 3.03 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: 0.480 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.370 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- 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= 0.343 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP B 218 HIS 0.005 0.001 HIS A 169 PHE 0.020 0.002 PHE B 221 TYR 0.026 0.003 TYR C 119 ARG 0.017 0.002 ARG A 376 *********************** 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 : 1.049 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 174 average time/residue: 1.3172 time to fit residues: 244.6486 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 : 1.019 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.074773 restraints weight = 16252.879| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.97 r_work: 0.2651 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9099 Z= 0.180 Angle : 0.540 8.815 12372 Z= 0.291 Chirality : 0.038 0.208 1440 Planarity : 0.004 0.040 1533 Dihedral : 4.618 24.072 1235 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Rotamer: Outliers : 2.02 % Allowed : 15.55 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1155 helix: 1.67 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 257 HIS 0.004 0.001 HIS C 323 PHE 0.019 0.001 PHE C 221 TYR 0.025 0.002 TYR A 119 ARG 0.004 0.001 ARG C 376 *********************** 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 162 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8469 (m-30) cc_final: 0.8239 (m-30) REVERT: A 259 GLN cc_start: 0.8116 (pt0) cc_final: 0.7346 (pp30) REVERT: A 339 ASP cc_start: 0.8104 (t0) cc_final: 0.7822 (t0) REVERT: B 64 MET cc_start: 0.8618 (ttt) cc_final: 0.8260 (ttt) REVERT: B 218 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.7485 (m-90) REVERT: B 339 ASP cc_start: 0.8134 (t0) cc_final: 0.7802 (t0) REVERT: C 161 ASP cc_start: 0.9179 (t70) cc_final: 0.8971 (t70) REVERT: C 259 GLN cc_start: 0.8136 (pt0) cc_final: 0.7888 (pp30) REVERT: C 339 ASP cc_start: 0.7982 (t0) cc_final: 0.7651 (t0) REVERT: C 341 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8523 (pp30) outliers start: 19 outliers final: 8 residues processed: 152 average time/residue: 1.2627 time to fit residues: 205.4010 Evaluate side-chains 135 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 341 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 45 ASN C 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.090034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.071252 restraints weight = 16793.339| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.00 r_work: 0.2614 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9099 Z= 0.196 Angle : 0.509 7.016 12372 Z= 0.277 Chirality : 0.039 0.185 1440 Planarity : 0.003 0.034 1533 Dihedral : 4.150 14.473 1227 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.08 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 16.61 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.25), residues: 1155 helix: 2.38 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 257 HIS 0.005 0.001 HIS B 323 PHE 0.014 0.001 PHE B 221 TYR 0.027 0.002 TYR B 119 ARG 0.004 0.000 ARG B 376 *********************** 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 153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9329 (mt-10) REVERT: A 156 GLN cc_start: 0.9019 (tt0) cc_final: 0.8556 (tm-30) REVERT: A 259 GLN cc_start: 0.8196 (pt0) cc_final: 0.7386 (pp30) REVERT: A 339 ASP cc_start: 0.8129 (t0) cc_final: 0.7810 (t0) REVERT: B 156 GLN cc_start: 0.9114 (tt0) cc_final: 0.8654 (tm-30) REVERT: B 339 ASP cc_start: 0.8188 (t0) cc_final: 0.7860 (t0) REVERT: B 399 GLU cc_start: 0.3775 (OUTLIER) cc_final: 0.3488 (pt0) REVERT: C 259 GLN cc_start: 0.8272 (pt0) cc_final: 0.7978 (pp30) REVERT: C 339 ASP cc_start: 0.8096 (t0) cc_final: 0.7650 (t0) REVERT: C 341 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8568 (pt0) outliers start: 20 outliers final: 12 residues processed: 144 average time/residue: 1.2442 time to fit residues: 191.6732 Evaluate side-chains 138 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 B residue 399 GLU Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 341 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.092959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.074092 restraints weight = 16457.435| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.99 r_work: 0.2644 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9099 Z= 0.160 Angle : 0.506 7.222 12372 Z= 0.270 Chirality : 0.038 0.181 1440 Planarity : 0.003 0.031 1533 Dihedral : 4.073 15.548 1227 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.75 % Rotamer: Outliers : 1.81 % Allowed : 17.78 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1155 helix: 2.64 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.98 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 257 HIS 0.005 0.001 HIS B 323 PHE 0.024 0.001 PHE B 221 TYR 0.020 0.001 TYR A 119 ARG 0.003 0.000 ARG B 376 *********************** 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 148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9295 (mt-10) REVERT: A 156 GLN cc_start: 0.9029 (tt0) cc_final: 0.8562 (tm-30) REVERT: A 259 GLN cc_start: 0.8284 (pt0) cc_final: 0.7505 (pp30) REVERT: A 339 ASP cc_start: 0.8123 (t0) cc_final: 0.7781 (t0) REVERT: A 399 GLU cc_start: 0.5199 (pm20) cc_final: 0.4887 (pt0) REVERT: B 156 GLN cc_start: 0.9111 (tt0) cc_final: 0.8635 (tm-30) REVERT: B 339 ASP cc_start: 0.8173 (t0) cc_final: 0.7832 (t0) REVERT: C 259 GLN cc_start: 0.8273 (pt0) cc_final: 0.7984 (pp30) REVERT: C 339 ASP cc_start: 0.8095 (t0) cc_final: 0.7641 (t0) REVERT: C 341 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8689 (pt0) outliers start: 17 outliers final: 14 residues processed: 142 average time/residue: 1.2365 time to fit residues: 188.0619 Evaluate side-chains 136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 341 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 258 GLN B 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.090360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.071592 restraints weight = 16795.746| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.01 r_work: 0.2602 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9099 Z= 0.200 Angle : 0.507 7.541 12372 Z= 0.273 Chirality : 0.038 0.177 1440 Planarity : 0.003 0.030 1533 Dihedral : 3.993 15.285 1227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Rotamer: Outliers : 1.81 % Allowed : 18.32 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1155 helix: 2.75 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.91 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 PHE 0.023 0.001 PHE B 221 TYR 0.024 0.002 TYR B 119 ARG 0.003 0.000 ARG B 376 *********************** 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 142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.9052 (tt0) cc_final: 0.8582 (tm-30) REVERT: A 339 ASP cc_start: 0.8177 (t0) cc_final: 0.7833 (t0) REVERT: A 399 GLU cc_start: 0.5172 (pm20) cc_final: 0.4840 (pt0) REVERT: B 156 GLN cc_start: 0.9121 (tt0) cc_final: 0.8649 (tm-30) REVERT: B 161 ASP cc_start: 0.9013 (t0) cc_final: 0.8674 (t0) REVERT: B 339 ASP cc_start: 0.8205 (t0) cc_final: 0.7852 (t0) REVERT: C 156 GLN cc_start: 0.9092 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 218 TRP cc_start: 0.8825 (OUTLIER) cc_final: 0.7719 (t-100) REVERT: C 259 GLN cc_start: 0.8324 (pt0) cc_final: 0.8007 (pp30) REVERT: C 339 ASP cc_start: 0.8162 (t0) cc_final: 0.7698 (t0) REVERT: C 341 GLN cc_start: 0.8986 (pt0) cc_final: 0.8645 (pt0) outliers start: 17 outliers final: 11 residues processed: 139 average time/residue: 1.3278 time to fit residues: 197.5014 Evaluate side-chains 130 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.089500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.070673 restraints weight = 16685.347| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.00 r_work: 0.2593 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2562 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= 0.210 Angle : 0.523 8.233 12372 Z= 0.280 Chirality : 0.038 0.181 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.989 15.929 1227 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Rotamer: Outliers : 1.92 % Allowed : 18.64 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.25), residues: 1155 helix: 2.81 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.003 0.001 HIS B 323 PHE 0.024 0.001 PHE C 221 TYR 0.022 0.002 TYR C 119 ARG 0.002 0.000 ARG B 376 *********************** 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 143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.082 Fit side-chains REVERT: A 156 GLN cc_start: 0.9060 (tt0) cc_final: 0.8593 (tm-30) REVERT: A 259 GLN cc_start: 0.8206 (pt0) cc_final: 0.7450 (pp30) REVERT: A 339 ASP cc_start: 0.8199 (t0) cc_final: 0.7846 (t0) REVERT: B 156 GLN cc_start: 0.9112 (tt0) cc_final: 0.8646 (tm-30) REVERT: B 161 ASP cc_start: 0.8993 (t0) cc_final: 0.8672 (t0) REVERT: B 259 GLN cc_start: 0.8297 (pt0) cc_final: 0.7631 (pp30) REVERT: B 339 ASP cc_start: 0.8301 (t0) cc_final: 0.7914 (t0) REVERT: B 399 GLU cc_start: 0.3840 (OUTLIER) cc_final: 0.3573 (pt0) REVERT: C 156 GLN cc_start: 0.9093 (tt0) cc_final: 0.8643 (tm-30) REVERT: C 218 TRP cc_start: 0.9015 (OUTLIER) cc_final: 0.7441 (t-100) REVERT: C 259 GLN cc_start: 0.8397 (pt0) cc_final: 0.8090 (pp30) REVERT: C 339 ASP cc_start: 0.8201 (t0) cc_final: 0.7592 (t0) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 1.2936 time to fit residues: 193.5076 Evaluate side-chains 132 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 278 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 95 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.073533 restraints weight = 16795.317| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.99 r_work: 0.2643 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9099 Z= 0.165 Angle : 0.513 8.887 12372 Z= 0.274 Chirality : 0.038 0.182 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.963 15.458 1227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.16 % Favored : 97.58 % Rotamer: Outliers : 2.02 % Allowed : 19.06 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.25), residues: 1155 helix: 2.92 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.07 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 257 HIS 0.004 0.001 HIS B 323 PHE 0.025 0.001 PHE A 221 TYR 0.028 0.002 TYR B 119 ARG 0.002 0.000 ARG B 376 *********************** 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 147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.9069 (tt0) cc_final: 0.8586 (tm-30) REVERT: A 259 GLN cc_start: 0.8260 (pt0) cc_final: 0.7545 (pp30) REVERT: A 339 ASP cc_start: 0.8174 (t0) cc_final: 0.7820 (t0) REVERT: B 156 GLN cc_start: 0.9118 (tt0) cc_final: 0.8646 (tm-30) REVERT: B 161 ASP cc_start: 0.8955 (t0) cc_final: 0.8622 (t0) REVERT: B 339 ASP cc_start: 0.8252 (t0) cc_final: 0.7892 (t0) REVERT: B 399 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.3490 (pt0) REVERT: C 156 GLN cc_start: 0.9134 (tt0) cc_final: 0.8678 (tm-30) REVERT: C 218 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8004 (t-100) REVERT: C 259 GLN cc_start: 0.8380 (pt0) cc_final: 0.8077 (pp30) REVERT: C 339 ASP cc_start: 0.8202 (t0) cc_final: 0.7632 (t0) outliers start: 19 outliers final: 11 residues processed: 142 average time/residue: 1.2741 time to fit residues: 193.5555 Evaluate side-chains 130 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 ASN B 22 GLN B 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.073041 restraints weight = 16918.891| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.01 r_work: 0.2640 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9099 Z= 0.178 Angle : 0.524 8.866 12372 Z= 0.280 Chirality : 0.038 0.186 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.924 16.412 1227 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 18.96 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.25), residues: 1155 helix: 2.95 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.003 0.001 HIS B 323 PHE 0.025 0.001 PHE A 221 TYR 0.021 0.001 TYR C 119 ARG 0.002 0.000 ARG B 376 *********************** 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 148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.919 Fit side-chains REVERT: A 156 GLN cc_start: 0.9056 (tt0) cc_final: 0.8561 (tm-30) REVERT: A 259 GLN cc_start: 0.8344 (pt0) cc_final: 0.7661 (pp30) REVERT: A 339 ASP cc_start: 0.8184 (t0) cc_final: 0.7832 (t0) REVERT: B 156 GLN cc_start: 0.9124 (tt0) cc_final: 0.8640 (tm-30) REVERT: B 259 GLN cc_start: 0.8314 (pt0) cc_final: 0.7649 (pp30) REVERT: B 339 ASP cc_start: 0.8303 (t0) cc_final: 0.7914 (t0) REVERT: B 399 GLU cc_start: 0.3828 (OUTLIER) cc_final: 0.3573 (pt0) REVERT: C 156 GLN cc_start: 0.9122 (tt0) cc_final: 0.8656 (tm-30) REVERT: C 218 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.8032 (t-100) REVERT: C 259 GLN cc_start: 0.8433 (pt0) cc_final: 0.7819 (pp30) REVERT: C 339 ASP cc_start: 0.8231 (t0) cc_final: 0.7643 (t0) REVERT: C 341 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8765 (pt0) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 1.2287 time to fit residues: 187.9693 Evaluate side-chains 139 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 191 ASN 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 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 Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 341 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** 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 = 0.3212 r_free = 0.3212 target = 0.097081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.079843 restraints weight = 16527.979| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.79 r_work: 0.2797 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9099 Z= 0.157 Angle : 0.524 9.679 12372 Z= 0.278 Chirality : 0.038 0.191 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.928 15.467 1227 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Rotamer: Outliers : 1.49 % Allowed : 19.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.25), residues: 1155 helix: 2.98 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.003 0.001 HIS B 323 PHE 0.026 0.001 PHE A 221 TYR 0.031 0.001 TYR B 119 ARG 0.002 0.000 ARG B 376 *********************** 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 148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.040 Fit side-chains REVERT: A 156 GLN cc_start: 0.9131 (tt0) cc_final: 0.8582 (tm-30) REVERT: A 202 ASP cc_start: 0.8552 (m-30) cc_final: 0.8317 (m-30) REVERT: A 221 PHE cc_start: 0.8100 (t80) cc_final: 0.7808 (t80) REVERT: A 259 GLN cc_start: 0.8466 (pt0) cc_final: 0.7762 (pp30) REVERT: A 339 ASP cc_start: 0.8319 (t0) cc_final: 0.7930 (t0) REVERT: B 156 GLN cc_start: 0.9132 (tt0) cc_final: 0.8610 (tm-30) REVERT: B 161 ASP cc_start: 0.8961 (t70) cc_final: 0.8711 (t0) REVERT: B 259 GLN cc_start: 0.8364 (pt0) cc_final: 0.7762 (pp30) REVERT: B 339 ASP cc_start: 0.8432 (t0) cc_final: 0.8045 (t0) REVERT: B 399 GLU cc_start: 0.3937 (OUTLIER) cc_final: 0.3716 (pt0) REVERT: C 156 GLN cc_start: 0.9162 (tt0) cc_final: 0.8684 (tm-30) REVERT: C 218 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.7924 (t-100) REVERT: C 259 GLN cc_start: 0.8453 (pt0) cc_final: 0.7963 (pp30) REVERT: C 339 ASP cc_start: 0.8359 (t0) cc_final: 0.7757 (t0) REVERT: C 341 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8845 (pt0) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 1.1982 time to fit residues: 186.2823 Evaluate side-chains 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 341 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN C 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.068297 restraints weight = 17079.354| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.00 r_work: 0.2564 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9099 Z= 0.264 Angle : 0.571 11.478 12372 Z= 0.304 Chirality : 0.040 0.185 1440 Planarity : 0.003 0.027 1533 Dihedral : 3.943 14.724 1227 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.16 % Favored : 97.58 % Rotamer: Outliers : 1.28 % Allowed : 20.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1155 helix: 2.87 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.003 0.001 HIS C 323 PHE 0.026 0.001 PHE A 221 TYR 0.023 0.002 TYR C 119 ARG 0.002 0.000 ARG C 376 ********************** 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 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.9047 (tt0) cc_final: 0.8602 (tm-30) REVERT: A 228 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7945 (ptpp) REVERT: A 259 GLN cc_start: 0.8379 (pt0) cc_final: 0.7686 (pp30) REVERT: A 339 ASP cc_start: 0.8289 (t0) cc_final: 0.7903 (t0) REVERT: B 80 TYR cc_start: 0.5990 (t80) cc_final: 0.5778 (t80) REVERT: B 156 GLN cc_start: 0.9123 (tt0) cc_final: 0.8642 (tm-30) REVERT: B 161 ASP cc_start: 0.8985 (t70) cc_final: 0.8716 (t0) REVERT: B 339 ASP cc_start: 0.8391 (t0) cc_final: 0.7981 (t0) REVERT: B 399 GLU cc_start: 0.3906 (OUTLIER) cc_final: 0.3706 (pt0) REVERT: C 156 GLN cc_start: 0.9101 (tt0) cc_final: 0.8659 (tm-30) REVERT: C 218 TRP cc_start: 0.9206 (OUTLIER) cc_final: 0.7145 (t-100) REVERT: C 259 GLN cc_start: 0.8448 (pt0) cc_final: 0.7840 (pp30) REVERT: C 339 ASP cc_start: 0.8320 (t0) cc_final: 0.7734 (t0) REVERT: C 341 GLN cc_start: 0.9122 (pt0) cc_final: 0.8761 (pt0) outliers start: 12 outliers final: 11 residues processed: 132 average time/residue: 1.3833 time to fit residues: 194.5653 Evaluate side-chains 133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 B residue 399 GLU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 231 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.071039 restraints weight = 16692.906| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.99 r_work: 0.2617 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9099 Z= 0.177 Angle : 0.553 12.172 12372 Z= 0.292 Chirality : 0.039 0.189 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.967 15.722 1227 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.51 % Favored : 97.23 % Rotamer: Outliers : 1.28 % Allowed : 20.45 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1155 helix: 2.99 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 257 HIS 0.004 0.001 HIS B 323 PHE 0.026 0.001 PHE A 221 TYR 0.029 0.002 TYR B 119 ARG 0.002 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.55 seconds wall clock time: 106 minutes 20.59 seconds (6380.59 seconds total)