Starting phenix.real_space_refine on Thu Jul 2 08:28:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.map" model { file = "/net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oic_70519/07_2026/9oic_70519.cif" } resolution = 3.48 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 36 5.16 5 C 5104 2.51 5 N 1212 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7594 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Chain: "C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Chain: "D" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Time building chain proxies: 1.42, per 1000 atoms: 0.19 Number of scatterers: 7594 At special positions: 0 Unit cell: (110.24, 111.3, 76.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 36 16.00 O 1240 8.00 N 1212 7.00 C 5104 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: 0.41 Conformation dependent library (CDL) restraints added in 265.4 milliseconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 219 through 222 Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 277 through 301 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.559A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 331 removed outlier: 3.947A pdb=" N ASP A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.599A pdb=" N THR A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.509A pdb=" N ILE A 364 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.577A pdb=" N ILE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.146A pdb=" N HIS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 428 through 441 removed outlier: 3.988A pdb=" N TRP A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 223 through 248 removed outlier: 4.250A pdb=" N THR B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 301 Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 310 through 331 removed outlier: 3.889A pdb=" N ASP B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Proline residue: B 322 - end of helix removed outlier: 3.660A pdb=" N THR B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.825A pdb=" N VAL B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.948A pdb=" N HIS B 378 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 392 through 418 Processing helix chain 'B' and resid 428 through 441 removed outlier: 4.624A pdb=" N TRP B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 removed outlier: 3.805A pdb=" N ALA B 471 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 223 through 248 removed outlier: 4.230A pdb=" N THR C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 301 removed outlier: 3.684A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.611A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 331 removed outlier: 3.942A pdb=" N ASP C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.594A pdb=" N THR C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.761A pdb=" N ARG C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 374 through 379 removed outlier: 4.049A pdb=" N HIS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.645A pdb=" N GLN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 418 Processing helix chain 'C' and resid 428 through 441 removed outlier: 3.991A pdb=" N TRP C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 223 through 248 removed outlier: 4.183A pdb=" N THR D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 301 Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.554A pdb=" N PHE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 331 removed outlier: 3.940A pdb=" N ASP D 316 " --> pdb=" O MET D 312 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.598A pdb=" N THR D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 374 through 379 removed outlier: 4.050A pdb=" N HIS D 378 " --> pdb=" O LYS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.682A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 428 through 441 removed outlier: 3.983A pdb=" N TRP D 434 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 478 502 hydrogen bonds defined for protein. 1464 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: 0.73 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2247 1.34 - 1.46: 1982 1.46 - 1.58: 3511 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7792 Sorted by residual: bond pdb=" C LEU A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 1.334 1.352 -0.018 8.40e-03 1.42e+04 4.69e+00 bond pdb=" CD ARG D 384 " pdb=" NE ARG D 384 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.46e+00 bond pdb=" CB GLU B 221 " pdb=" CG GLU B 221 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CB GLU D 221 " pdb=" CG GLU D 221 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB GLU C 221 " pdb=" CG GLU C 221 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 ... (remaining 7787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10336 1.69 - 3.39: 194 3.39 - 5.08: 48 5.08 - 6.77: 15 6.77 - 8.47: 3 Bond angle restraints: 10596 Sorted by residual: angle pdb=" CA GLU C 221 " pdb=" CB GLU C 221 " pdb=" CG GLU C 221 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.21e+00 angle pdb=" CB LYS A 380 " pdb=" CG LYS A 380 " pdb=" CD LYS A 380 " ideal model delta sigma weight residual 111.30 118.17 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" CB GLU B 221 " pdb=" CG GLU B 221 " pdb=" CD GLU B 221 " ideal model delta sigma weight residual 112.60 117.66 -5.06 1.70e+00 3.46e-01 8.86e+00 angle pdb=" CA GLU D 221 " pdb=" CB GLU D 221 " pdb=" CG GLU D 221 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.83e+00 angle pdb=" CA LYS A 380 " pdb=" CB LYS A 380 " pdb=" CG LYS A 380 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.82e+00 ... (remaining 10591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 3739 14.13 - 28.26: 534 28.26 - 42.39: 174 42.39 - 56.52: 65 56.52 - 70.65: 4 Dihedral angle restraints: 4516 sinusoidal: 1756 harmonic: 2760 Sorted by residual: dihedral pdb=" CA ASN B 480 " pdb=" C ASN B 480 " pdb=" N PHE B 481 " pdb=" CA PHE B 481 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ASN D 480 " pdb=" C ASN D 480 " pdb=" N PHE D 481 " pdb=" CA PHE D 481 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ASN A 480 " pdb=" C ASN A 480 " pdb=" N PHE A 481 " pdb=" CA PHE A 481 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 780 0.030 - 0.060: 334 0.060 - 0.090: 104 0.090 - 0.119: 48 0.119 - 0.149: 2 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CG LEU D 215 " pdb=" CB LEU D 215 " pdb=" CD1 LEU D 215 " pdb=" CD2 LEU D 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CG LEU A 215 " pdb=" CB LEU A 215 " pdb=" CD1 LEU A 215 " pdb=" CD2 LEU A 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE B 321 " pdb=" N ILE B 321 " pdb=" C ILE B 321 " pdb=" CB ILE B 321 " both_signs ideal model delta sigma weight residual False 2.43 2.32 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 1265 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 221 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" CD GLU A 221 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU A 221 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 221 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 221 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" CD GLU C 221 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 221 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 221 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 221 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" CD GLU D 221 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU D 221 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 221 " 0.012 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.51 - 3.03: 4866 3.03 - 3.56: 9884 3.56 - 4.09: 12709 4.09 - 4.61: 20172 4.61 - 5.14: 25482 Nonbonded interactions: 73113 Sorted by model distance: nonbonded pdb=" N GLU D 221 " pdb=" OE1 GLU D 221 " model vdw 2.507 3.120 nonbonded pdb=" N GLU B 221 " pdb=" OE1 GLU B 221 " model vdw 2.507 3.120 nonbonded pdb=" N GLU A 221 " pdb=" OE1 GLU A 221 " model vdw 2.507 3.120 nonbonded pdb=" N GLU C 221 " pdb=" OE1 GLU C 221 " model vdw 2.511 3.120 nonbonded pdb=" OE2 GLU A 395 " pdb=" NH2 ARG D 384 " model vdw 2.538 3.120 ... (remaining 73108 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 210 through 487) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7792 Z= 0.145 Angle : 0.608 8.466 10596 Z= 0.316 Chirality : 0.039 0.149 1268 Planarity : 0.003 0.026 1268 Dihedral : 15.699 70.651 2716 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.59 % Allowed : 25.96 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 920 helix: 1.19 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 384 TYR 0.025 0.001 TYR B 323 PHE 0.007 0.001 PHE C 410 TRP 0.008 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7792) covalent geometry : angle 0.60780 / 0.32 (10596) hydrogen bonds : bond 0.14562 / 9.51 ( 502) hydrogen bonds : angle 4.85087 / 3.46 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.203 Fit side-chains REVERT: A 218 GLU cc_start: 0.8267 (tp30) cc_final: 0.7934 (tp30) REVERT: A 323 TYR cc_start: 0.9180 (t80) cc_final: 0.8897 (t80) REVERT: A 362 ARG cc_start: 0.4382 (ptt90) cc_final: 0.3596 (ptt180) REVERT: A 383 GLN cc_start: 0.8988 (mt0) cc_final: 0.8561 (mt0) REVERT: A 390 LYS cc_start: 0.9563 (tmtt) cc_final: 0.8728 (mptt) REVERT: A 431 ASP cc_start: 0.8627 (m-30) cc_final: 0.7878 (m-30) REVERT: B 383 GLN cc_start: 0.8815 (mt0) cc_final: 0.8246 (mp10) REVERT: B 390 LYS cc_start: 0.9492 (tmtt) cc_final: 0.8644 (mptt) REVERT: C 383 GLN cc_start: 0.8584 (mt0) cc_final: 0.7860 (mp10) REVERT: C 390 LYS cc_start: 0.9434 (tmtt) cc_final: 0.8570 (mptt) REVERT: C 431 ASP cc_start: 0.8593 (m-30) cc_final: 0.7867 (m-30) REVERT: D 218 GLU cc_start: 0.8349 (tp30) cc_final: 0.8003 (tp30) REVERT: D 293 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8721 (tm-30) REVERT: D 362 ARG cc_start: 0.4198 (ptt90) cc_final: 0.3967 (ptt180) REVERT: D 383 GLN cc_start: 0.8567 (mt0) cc_final: 0.7925 (mp10) REVERT: D 390 LYS cc_start: 0.9533 (tmtt) cc_final: 0.8692 (mptt) REVERT: D 431 ASP cc_start: 0.8653 (m-30) cc_final: 0.7911 (m-30) outliers start: 30 outliers final: 24 residues processed: 171 average time/residue: 0.0646 time to fit residues: 15.1575 Evaluate side-chains 175 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0030 chunk 74 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080232 restraints weight = 18220.492| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.83 r_work: 0.3018 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7792 Z= 0.121 Angle : 0.524 5.622 10596 Z= 0.278 Chirality : 0.038 0.126 1268 Planarity : 0.003 0.027 1268 Dihedral : 6.980 58.111 1054 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.14 % Allowed : 22.37 % Favored : 72.49 % 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 are not related in a simple way. whole: 1.24 (0.28), residues: 920 helix: 1.30 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 394 TYR 0.009 0.001 TYR C 323 PHE 0.008 0.001 PHE C 410 TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7792) covalent geometry : angle 0.52371 / 0.28 (10596) hydrogen bonds : bond 0.04110 / 2.70 ( 502) hydrogen bonds : angle 4.04161 / 2.90 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.191 Fit side-chains REVERT: A 218 GLU cc_start: 0.8525 (tp30) cc_final: 0.8098 (tp30) REVERT: A 323 TYR cc_start: 0.9118 (t80) cc_final: 0.8894 (t80) REVERT: A 362 ARG cc_start: 0.5327 (ptt90) cc_final: 0.4423 (ptt90) REVERT: A 383 GLN cc_start: 0.9047 (mt0) cc_final: 0.8544 (mt0) REVERT: A 390 LYS cc_start: 0.9568 (tmtt) cc_final: 0.8665 (mptt) REVERT: A 431 ASP cc_start: 0.8846 (m-30) cc_final: 0.8161 (m-30) REVERT: B 218 GLU cc_start: 0.8681 (tp30) cc_final: 0.8447 (mm-30) REVERT: B 378 HIS cc_start: 0.9026 (m-70) cc_final: 0.8618 (m90) REVERT: B 383 GLN cc_start: 0.8897 (mt0) cc_final: 0.8291 (mt0) REVERT: B 390 LYS cc_start: 0.9527 (tmtt) cc_final: 0.8643 (mptt) REVERT: C 383 GLN cc_start: 0.8752 (mt0) cc_final: 0.8053 (mp10) REVERT: C 390 LYS cc_start: 0.9339 (tmtt) cc_final: 0.8376 (mptt) REVERT: C 431 ASP cc_start: 0.8905 (m-30) cc_final: 0.8239 (m-30) REVERT: D 218 GLU cc_start: 0.8611 (tp30) cc_final: 0.8236 (tp30) REVERT: D 293 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8770 (tm-30) REVERT: D 362 ARG cc_start: 0.5136 (ptt90) cc_final: 0.4452 (ptt180) REVERT: D 383 GLN cc_start: 0.8648 (mt0) cc_final: 0.8127 (mp10) REVERT: D 390 LYS cc_start: 0.9540 (tmtt) cc_final: 0.8653 (mptt) REVERT: D 431 ASP cc_start: 0.8892 (m-30) cc_final: 0.8208 (m-30) REVERT: D 481 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8536 (t80) outliers start: 43 outliers final: 27 residues processed: 189 average time/residue: 0.0647 time to fit residues: 16.8499 Evaluate side-chains 172 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.0040 chunk 90 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.101149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076118 restraints weight = 18729.673| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.20 r_work: 0.3083 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7792 Z= 0.115 Angle : 0.527 5.369 10596 Z= 0.276 Chirality : 0.039 0.208 1268 Planarity : 0.003 0.028 1268 Dihedral : 6.397 57.773 1037 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 22.37 % Favored : 73.80 % 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 are not related in a simple way. whole: 1.25 (0.28), residues: 920 helix: 1.23 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.62 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 394 TYR 0.014 0.001 TYR B 323 PHE 0.013 0.001 PHE C 404 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7792) covalent geometry : angle 0.52741 / 0.28 (10596) hydrogen bonds : bond 0.03731 / 2.45 ( 502) hydrogen bonds : angle 3.89518 / 2.81 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.322 Fit side-chains REVERT: A 218 GLU cc_start: 0.8650 (tp30) cc_final: 0.8165 (tp30) REVERT: A 362 ARG cc_start: 0.4928 (ptt90) cc_final: 0.3795 (ptt90) REVERT: A 380 LYS cc_start: 0.8916 (mppt) cc_final: 0.8655 (mppt) REVERT: A 383 GLN cc_start: 0.8942 (mt0) cc_final: 0.8409 (mt0) REVERT: A 390 LYS cc_start: 0.9481 (tmtt) cc_final: 0.8535 (mptt) REVERT: A 431 ASP cc_start: 0.8890 (m-30) cc_final: 0.8182 (m-30) REVERT: A 481 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8679 (t80) REVERT: B 218 GLU cc_start: 0.8815 (tp30) cc_final: 0.8546 (mm-30) REVERT: B 383 GLN cc_start: 0.8885 (mt0) cc_final: 0.8258 (mt0) REVERT: B 390 LYS cc_start: 0.9421 (tmtt) cc_final: 0.8472 (mptt) REVERT: B 438 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8869 (p) REVERT: C 383 GLN cc_start: 0.8734 (mt0) cc_final: 0.8055 (mp10) REVERT: C 390 LYS cc_start: 0.9286 (tmtt) cc_final: 0.8298 (mptt) REVERT: C 395 GLU cc_start: 0.8538 (mp0) cc_final: 0.8334 (mp0) REVERT: C 431 ASP cc_start: 0.8925 (m-30) cc_final: 0.8252 (m-30) REVERT: D 218 GLU cc_start: 0.8699 (tp30) cc_final: 0.8356 (tp30) REVERT: D 293 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8726 (tm-30) REVERT: D 362 ARG cc_start: 0.4930 (ptt90) cc_final: 0.4222 (ptt90) REVERT: D 383 GLN cc_start: 0.8654 (mt0) cc_final: 0.8119 (mp10) REVERT: D 390 LYS cc_start: 0.9513 (tmtt) cc_final: 0.8567 (mptt) REVERT: D 431 ASP cc_start: 0.8945 (m-30) cc_final: 0.8272 (m-30) REVERT: D 485 TYR cc_start: 0.6393 (m-80) cc_final: 0.6084 (m-80) outliers start: 32 outliers final: 19 residues processed: 179 average time/residue: 0.0813 time to fit residues: 19.9179 Evaluate side-chains 170 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 0.0010 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076763 restraints weight = 18915.232| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.23 r_work: 0.3092 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7792 Z= 0.113 Angle : 0.526 5.685 10596 Z= 0.275 Chirality : 0.038 0.145 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.512 58.143 1024 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.59 % Allowed : 24.16 % Favored : 72.25 % 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 are not related in a simple way. whole: 1.31 (0.28), residues: 920 helix: 1.26 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 384 TYR 0.017 0.001 TYR A 323 PHE 0.008 0.001 PHE C 410 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7792) covalent geometry : angle 0.52571 / 0.27 (10596) hydrogen bonds : bond 0.03599 / 2.36 ( 502) hydrogen bonds : angle 3.81309 / 2.74 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.302 Fit side-chains REVERT: A 218 GLU cc_start: 0.8642 (tp30) cc_final: 0.8172 (tp30) REVERT: A 362 ARG cc_start: 0.4906 (ptt90) cc_final: 0.3706 (ptt90) REVERT: A 390 LYS cc_start: 0.9462 (tmtt) cc_final: 0.8513 (mptt) REVERT: A 431 ASP cc_start: 0.8853 (m-30) cc_final: 0.8172 (m-30) REVERT: B 218 GLU cc_start: 0.8834 (tp30) cc_final: 0.8504 (tp30) REVERT: B 380 LYS cc_start: 0.8893 (mppt) cc_final: 0.8612 (mppt) REVERT: B 383 GLN cc_start: 0.8818 (mt0) cc_final: 0.8183 (mt0) REVERT: B 390 LYS cc_start: 0.9418 (tmtt) cc_final: 0.8466 (mptt) REVERT: C 323 TYR cc_start: 0.9314 (t80) cc_final: 0.8946 (t80) REVERT: C 383 GLN cc_start: 0.8777 (mt0) cc_final: 0.8170 (mp10) REVERT: C 390 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8336 (mptt) REVERT: C 431 ASP cc_start: 0.8927 (m-30) cc_final: 0.8280 (m-30) REVERT: D 218 GLU cc_start: 0.8706 (tp30) cc_final: 0.8370 (tp30) REVERT: D 293 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8717 (tm-30) REVERT: D 362 ARG cc_start: 0.4892 (ptt90) cc_final: 0.3857 (ptt90) REVERT: D 383 GLN cc_start: 0.8663 (mt0) cc_final: 0.8119 (mp10) REVERT: D 390 LYS cc_start: 0.9509 (tmtt) cc_final: 0.8564 (mptt) REVERT: D 431 ASP cc_start: 0.8948 (m-30) cc_final: 0.8277 (m-30) outliers start: 30 outliers final: 20 residues processed: 182 average time/residue: 0.0780 time to fit residues: 19.4431 Evaluate side-chains 174 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073149 restraints weight = 18956.571| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.13 r_work: 0.3025 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7792 Z= 0.186 Angle : 0.604 6.306 10596 Z= 0.313 Chirality : 0.040 0.144 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.222 51.247 1021 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.50 % Allowed : 22.85 % Favored : 71.65 % 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 are not related in a simple way. whole: 1.43 (0.28), residues: 920 helix: 1.34 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 362 TYR 0.015 0.002 TYR D 323 PHE 0.009 0.001 PHE A 373 TRP 0.007 0.001 TRP D 289 HIS 0.006 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 7792) covalent geometry : angle 0.60387 / 0.31 (10596) hydrogen bonds : bond 0.03750 / 2.47 ( 502) hydrogen bonds : angle 3.96305 / 2.87 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.222 Fit side-chains REVERT: A 218 GLU cc_start: 0.8686 (tp30) cc_final: 0.8169 (tp30) REVERT: A 323 TYR cc_start: 0.9333 (t80) cc_final: 0.9079 (t80) REVERT: A 362 ARG cc_start: 0.5131 (ptt90) cc_final: 0.3919 (ptt180) REVERT: A 380 LYS cc_start: 0.8893 (mppt) cc_final: 0.8624 (mppt) REVERT: A 383 GLN cc_start: 0.8887 (mt0) cc_final: 0.8435 (mt0) REVERT: A 390 LYS cc_start: 0.9475 (tmtt) cc_final: 0.8571 (mptt) REVERT: A 431 ASP cc_start: 0.8925 (m-30) cc_final: 0.8193 (m-30) REVERT: B 218 GLU cc_start: 0.8882 (tp30) cc_final: 0.8543 (tp30) REVERT: B 390 LYS cc_start: 0.9466 (tmtt) cc_final: 0.8590 (mptt) REVERT: C 323 TYR cc_start: 0.9446 (t80) cc_final: 0.9105 (t80) REVERT: C 383 GLN cc_start: 0.8778 (mt0) cc_final: 0.8163 (mp10) REVERT: C 390 LYS cc_start: 0.9428 (tmtt) cc_final: 0.8503 (mptt) REVERT: C 431 ASP cc_start: 0.8996 (m-30) cc_final: 0.8330 (m-30) REVERT: D 218 GLU cc_start: 0.8701 (tp30) cc_final: 0.8339 (tp30) REVERT: D 293 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 362 ARG cc_start: 0.5051 (ptt90) cc_final: 0.4221 (ptt90) REVERT: D 383 GLN cc_start: 0.8714 (mt0) cc_final: 0.8182 (mp10) REVERT: D 390 LYS cc_start: 0.9543 (tmtt) cc_final: 0.8633 (mptt) REVERT: D 431 ASP cc_start: 0.9053 (m-30) cc_final: 0.8350 (m-30) outliers start: 46 outliers final: 40 residues processed: 175 average time/residue: 0.0626 time to fit residues: 15.0294 Evaluate side-chains 181 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075468 restraints weight = 18794.205| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.20 r_work: 0.3067 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7792 Z= 0.123 Angle : 0.565 6.168 10596 Z= 0.292 Chirality : 0.039 0.148 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.222 50.847 1021 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.19 % Allowed : 25.48 % Favored : 70.33 % 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 are not related in a simple way. whole: 1.43 (0.28), residues: 920 helix: 1.34 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.015 0.001 TYR D 323 PHE 0.008 0.001 PHE C 410 TRP 0.008 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7792) covalent geometry : angle 0.56512 / 0.29 (10596) hydrogen bonds : bond 0.03573 / 2.35 ( 502) hydrogen bonds : angle 3.82571 / 2.76 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.178 Fit side-chains REVERT: A 218 GLU cc_start: 0.8611 (tp30) cc_final: 0.8152 (tp30) REVERT: A 323 TYR cc_start: 0.9316 (t80) cc_final: 0.9081 (t80) REVERT: A 362 ARG cc_start: 0.4988 (ptt90) cc_final: 0.3792 (ptt180) REVERT: A 390 LYS cc_start: 0.9455 (tmtt) cc_final: 0.8469 (mmtt) REVERT: A 431 ASP cc_start: 0.8863 (m-30) cc_final: 0.8130 (m-30) REVERT: B 218 GLU cc_start: 0.8882 (tp30) cc_final: 0.8592 (mm-30) REVERT: B 383 GLN cc_start: 0.8817 (mt0) cc_final: 0.8159 (mt0) REVERT: B 390 LYS cc_start: 0.9423 (tmtt) cc_final: 0.8490 (mptt) REVERT: C 323 TYR cc_start: 0.9439 (t80) cc_final: 0.9130 (t80) REVERT: C 383 GLN cc_start: 0.8705 (mt0) cc_final: 0.8053 (mp10) REVERT: C 390 LYS cc_start: 0.9390 (tmtt) cc_final: 0.8473 (mptt) REVERT: C 405 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8779 (tp) REVERT: C 431 ASP cc_start: 0.8940 (m-30) cc_final: 0.8215 (m-30) REVERT: D 218 GLU cc_start: 0.8637 (tp30) cc_final: 0.8279 (tp30) REVERT: D 293 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8728 (tm-30) REVERT: D 362 ARG cc_start: 0.4990 (ptt90) cc_final: 0.3704 (ptt180) REVERT: D 383 GLN cc_start: 0.8676 (mt0) cc_final: 0.8164 (mp10) REVERT: D 390 LYS cc_start: 0.9515 (tmtt) cc_final: 0.8644 (mptt) REVERT: D 431 ASP cc_start: 0.8991 (m-30) cc_final: 0.8295 (m-30) outliers start: 35 outliers final: 29 residues processed: 178 average time/residue: 0.0656 time to fit residues: 16.0709 Evaluate side-chains 179 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.114370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089627 restraints weight = 18291.809| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.28 r_work: 0.3034 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7792 Z= 0.138 Angle : 0.597 6.757 10596 Z= 0.309 Chirality : 0.039 0.154 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.206 51.097 1021 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.67 % Allowed : 25.60 % Favored : 69.74 % 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 are not related in a simple way. whole: 1.45 (0.28), residues: 920 helix: 1.35 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.012 0.001 TYR B 323 PHE 0.007 0.001 PHE C 410 TRP 0.007 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7792) covalent geometry : angle 0.59684 / 0.31 (10596) hydrogen bonds : bond 0.03569 / 2.34 ( 502) hydrogen bonds : angle 3.82877 / 2.76 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.348 Fit side-chains REVERT: A 218 GLU cc_start: 0.8535 (tp30) cc_final: 0.8074 (tp30) REVERT: A 362 ARG cc_start: 0.4997 (ptt90) cc_final: 0.3796 (ptt180) REVERT: A 383 GLN cc_start: 0.8869 (mt0) cc_final: 0.8441 (mt0) REVERT: A 390 LYS cc_start: 0.9437 (tmtt) cc_final: 0.8478 (mmtt) REVERT: A 431 ASP cc_start: 0.8861 (m-30) cc_final: 0.8170 (m-30) REVERT: B 218 GLU cc_start: 0.8871 (tp30) cc_final: 0.8583 (mm-30) REVERT: B 383 GLN cc_start: 0.8814 (mt0) cc_final: 0.8156 (mt0) REVERT: B 390 LYS cc_start: 0.9432 (tmtt) cc_final: 0.8518 (mptt) REVERT: C 323 TYR cc_start: 0.9433 (t80) cc_final: 0.9163 (t80) REVERT: C 383 GLN cc_start: 0.8713 (mt0) cc_final: 0.8052 (mp10) REVERT: C 390 LYS cc_start: 0.9400 (tmtt) cc_final: 0.8500 (mptt) REVERT: C 405 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8858 (tp) REVERT: C 431 ASP cc_start: 0.8952 (m-30) cc_final: 0.8252 (m-30) REVERT: D 218 GLU cc_start: 0.8582 (tp30) cc_final: 0.8228 (tp30) REVERT: D 293 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8556 (tm-30) REVERT: D 323 TYR cc_start: 0.9346 (t80) cc_final: 0.8898 (t80) REVERT: D 362 ARG cc_start: 0.5110 (ptt90) cc_final: 0.3776 (ptt180) REVERT: D 383 GLN cc_start: 0.8680 (mt0) cc_final: 0.8190 (mp10) REVERT: D 390 LYS cc_start: 0.9526 (tmtt) cc_final: 0.8652 (mptt) REVERT: D 431 ASP cc_start: 0.8981 (m-30) cc_final: 0.8282 (m-30) outliers start: 39 outliers final: 34 residues processed: 179 average time/residue: 0.0726 time to fit residues: 17.9274 Evaluate side-chains 184 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072830 restraints weight = 18556.950| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.31 r_work: 0.2830 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7792 Z= 0.131 Angle : 0.600 7.385 10596 Z= 0.310 Chirality : 0.039 0.152 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.163 51.122 1021 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.67 % Allowed : 26.44 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.28), residues: 920 helix: 1.36 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 371 TYR 0.011 0.001 TYR B 323 PHE 0.008 0.001 PHE C 410 TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7792) covalent geometry : angle 0.60004 / 0.31 (10596) hydrogen bonds : bond 0.03509 / 2.30 ( 502) hydrogen bonds : angle 3.80680 / 2.75 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8788 (tp30) cc_final: 0.8275 (tp30) REVERT: A 323 TYR cc_start: 0.9245 (t80) cc_final: 0.8939 (t80) REVERT: A 362 ARG cc_start: 0.4078 (ptt90) cc_final: 0.3158 (ptt180) REVERT: A 383 GLN cc_start: 0.8748 (mt0) cc_final: 0.8317 (mt0) REVERT: A 390 LYS cc_start: 0.9340 (tmtt) cc_final: 0.8362 (mmtt) REVERT: A 431 ASP cc_start: 0.8906 (m-30) cc_final: 0.8186 (m-30) REVERT: B 218 GLU cc_start: 0.8887 (tp30) cc_final: 0.8589 (mm-30) REVERT: B 323 TYR cc_start: 0.9368 (t80) cc_final: 0.9143 (t80) REVERT: B 383 GLN cc_start: 0.8697 (mt0) cc_final: 0.8241 (mt0) REVERT: B 390 LYS cc_start: 0.9342 (tmtt) cc_final: 0.8391 (mptt) REVERT: C 323 TYR cc_start: 0.9384 (t80) cc_final: 0.9102 (t80) REVERT: C 383 GLN cc_start: 0.8614 (mt0) cc_final: 0.7976 (mp10) REVERT: C 390 LYS cc_start: 0.9325 (tmtt) cc_final: 0.8411 (mptt) REVERT: C 405 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8591 (tp) REVERT: C 431 ASP cc_start: 0.8962 (m-30) cc_final: 0.8254 (m-30) REVERT: D 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8355 (tp30) REVERT: D 293 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 323 TYR cc_start: 0.9304 (t80) cc_final: 0.8754 (t80) REVERT: D 362 ARG cc_start: 0.4068 (ptt90) cc_final: 0.3103 (ptt180) REVERT: D 383 GLN cc_start: 0.8582 (mt0) cc_final: 0.8058 (mp10) REVERT: D 390 LYS cc_start: 0.9448 (tmtt) cc_final: 0.8554 (mptt) REVERT: D 431 ASP cc_start: 0.9036 (m-30) cc_final: 0.8305 (m-30) outliers start: 39 outliers final: 31 residues processed: 181 average time/residue: 0.0719 time to fit residues: 17.6983 Evaluate side-chains 184 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.086875 restraints weight = 18127.828| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.35 r_work: 0.2851 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7792 Z= 0.128 Angle : 0.624 7.844 10596 Z= 0.321 Chirality : 0.039 0.160 1268 Planarity : 0.003 0.029 1268 Dihedral : 5.144 51.286 1021 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.95 % Allowed : 26.91 % Favored : 69.14 % 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 are not related in a simple way. whole: 1.45 (0.28), residues: 920 helix: 1.36 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.50 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 368 TYR 0.010 0.001 TYR A 323 PHE 0.008 0.001 PHE C 410 TRP 0.008 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7792) covalent geometry : angle 0.62364 / 0.32 (10596) hydrogen bonds : bond 0.03446 / 2.25 ( 502) hydrogen bonds : angle 3.74942 / 2.71 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.323 Fit side-chains REVERT: A 218 GLU cc_start: 0.8727 (tp30) cc_final: 0.8220 (tp30) REVERT: A 243 ILE cc_start: 0.8605 (mm) cc_final: 0.8394 (tp) REVERT: A 323 TYR cc_start: 0.9278 (t80) cc_final: 0.8969 (t80) REVERT: A 362 ARG cc_start: 0.3986 (ptt90) cc_final: 0.3099 (ptt90) REVERT: A 383 GLN cc_start: 0.8747 (mt0) cc_final: 0.8295 (mt0) REVERT: A 390 LYS cc_start: 0.9324 (tmtt) cc_final: 0.8346 (mmtt) REVERT: A 431 ASP cc_start: 0.8871 (m-30) cc_final: 0.8147 (m-30) REVERT: B 218 GLU cc_start: 0.8886 (tp30) cc_final: 0.8585 (mm-30) REVERT: B 323 TYR cc_start: 0.9378 (t80) cc_final: 0.9117 (t80) REVERT: B 383 GLN cc_start: 0.8673 (mt0) cc_final: 0.8211 (mt0) REVERT: B 390 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8383 (mptt) REVERT: C 323 TYR cc_start: 0.9360 (t80) cc_final: 0.9108 (t80) REVERT: C 383 GLN cc_start: 0.8590 (mt0) cc_final: 0.7962 (mp10) REVERT: C 390 LYS cc_start: 0.9304 (tmtt) cc_final: 0.8428 (mptt) REVERT: C 405 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 431 ASP cc_start: 0.8909 (m-30) cc_final: 0.8236 (m-30) REVERT: D 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8330 (tp30) REVERT: D 293 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8354 (tm-30) REVERT: D 323 TYR cc_start: 0.9308 (t80) cc_final: 0.8830 (t80) REVERT: D 362 ARG cc_start: 0.4028 (ptt90) cc_final: 0.3056 (ptt180) REVERT: D 383 GLN cc_start: 0.8577 (mt0) cc_final: 0.8059 (mp10) REVERT: D 390 LYS cc_start: 0.9440 (tmtt) cc_final: 0.8546 (mptt) REVERT: D 431 ASP cc_start: 0.8998 (m-30) cc_final: 0.8248 (m-30) outliers start: 33 outliers final: 24 residues processed: 179 average time/residue: 0.0747 time to fit residues: 18.4180 Evaluate side-chains 180 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.087177 restraints weight = 18089.066| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.33 r_work: 0.2852 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7792 Z= 0.131 Angle : 0.627 7.839 10596 Z= 0.322 Chirality : 0.039 0.167 1268 Planarity : 0.003 0.028 1268 Dihedral : 4.979 51.337 1017 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.71 % Allowed : 26.67 % Favored : 69.62 % 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 are not related in a simple way. whole: 1.45 (0.28), residues: 920 helix: 1.36 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.021 0.001 TYR C 219 PHE 0.008 0.001 PHE C 410 TRP 0.008 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7792) covalent geometry : angle 0.62749 / 0.32 (10596) hydrogen bonds : bond 0.03426 / 2.25 ( 502) hydrogen bonds : angle 3.74677 / 2.71 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8211 (tp30) REVERT: A 243 ILE cc_start: 0.8594 (mm) cc_final: 0.8392 (tp) REVERT: A 323 TYR cc_start: 0.9277 (t80) cc_final: 0.8934 (t80) REVERT: A 362 ARG cc_start: 0.4105 (ptt90) cc_final: 0.3147 (ptt90) REVERT: A 383 GLN cc_start: 0.8756 (mt0) cc_final: 0.8302 (mt0) REVERT: A 390 LYS cc_start: 0.9320 (tmtt) cc_final: 0.8343 (mmtt) REVERT: A 431 ASP cc_start: 0.8873 (m-30) cc_final: 0.8148 (m-30) REVERT: B 218 GLU cc_start: 0.8876 (tp30) cc_final: 0.8580 (mm-30) REVERT: B 323 TYR cc_start: 0.9378 (t80) cc_final: 0.9137 (t80) REVERT: B 383 GLN cc_start: 0.8679 (mt0) cc_final: 0.8210 (mt0) REVERT: B 390 LYS cc_start: 0.9332 (tmtt) cc_final: 0.8376 (mptt) REVERT: C 323 TYR cc_start: 0.9339 (t80) cc_final: 0.9078 (t80) REVERT: C 383 GLN cc_start: 0.8592 (mt0) cc_final: 0.7965 (mp10) REVERT: C 390 LYS cc_start: 0.9302 (tmtt) cc_final: 0.8430 (mptt) REVERT: C 405 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8526 (tp) REVERT: C 431 ASP cc_start: 0.8915 (m-30) cc_final: 0.8244 (m-30) REVERT: D 218 GLU cc_start: 0.8701 (tp30) cc_final: 0.8341 (tp30) REVERT: D 293 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 323 TYR cc_start: 0.9237 (t80) cc_final: 0.8792 (t80) REVERT: D 362 ARG cc_start: 0.4056 (ptt90) cc_final: 0.3084 (ptt180) REVERT: D 383 GLN cc_start: 0.8579 (mt0) cc_final: 0.8070 (mp10) REVERT: D 390 LYS cc_start: 0.9442 (tmtt) cc_final: 0.8553 (mptt) REVERT: D 431 ASP cc_start: 0.8962 (m-30) cc_final: 0.8215 (m-30) outliers start: 31 outliers final: 29 residues processed: 180 average time/residue: 0.0759 time to fit residues: 18.6340 Evaluate side-chains 185 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 481 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086969 restraints weight = 18181.242| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.37 r_work: 0.2844 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7792 Z= 0.139 Angle : 0.640 7.853 10596 Z= 0.329 Chirality : 0.039 0.166 1268 Planarity : 0.003 0.028 1268 Dihedral : 4.991 51.355 1017 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.31 % Allowed : 25.96 % Favored : 69.74 % 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 are not related in a simple way. whole: 1.48 (0.28), residues: 920 helix: 1.38 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 368 TYR 0.021 0.001 TYR C 255 PHE 0.007 0.001 PHE C 410 TRP 0.007 0.001 TRP D 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7792) covalent geometry : angle 0.63996 / 0.33 (10596) hydrogen bonds : bond 0.03458 / 2.28 ( 502) hydrogen bonds : angle 3.74604 / 2.71 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.83 seconds wall clock time: 25 minutes 28.13 seconds (1528.13 seconds total)