Starting phenix.real_space_refine on Tue Feb 3 23:24:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oic_70519/02_2026/9oic_70519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oic_70519/02_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_70519/02_2026/9oic_70519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oic_70519/02_2026/9oic_70519.map" model { file = "/net/cci-nas-00/data/ceres_data/9oic_70519/02_2026/9oic_70519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oic_70519/02_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-2.0-5952/lib/python3.9/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, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.31, per 1000 atoms: 0.17 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: 0.74 Conformation dependent library (CDL) restraints added in 252.0 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: 0.14 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: 1.10 Time building geometry restraints manager: 0.96 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: 1.380 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 covalent geometry : bond 0.00327 ( 7792) covalent geometry : angle 0.60780 (10596) hydrogen bonds : bond 0.14562 ( 502) hydrogen bonds : angle 4.85087 ( 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 : 0.295 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: 0.0737 time to fit residues: 17.1866 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 : 0.184 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080978 restraints weight = 18100.335| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.80 r_work: 0.3014 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0781 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= 0.117 Angle : 0.507 5.272 10596 Z= 0.269 Chirality : 0.038 0.125 1268 Planarity : 0.003 0.027 1268 Dihedral : 6.961 58.112 1054 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.67 % Allowed : 22.61 % Favored : 72.73 % 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: 1.31 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -0.89 (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 D 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 covalent geometry : bond 0.00244 ( 7792) covalent geometry : angle 0.50676 (10596) hydrogen bonds : bond 0.04235 ( 502) hydrogen bonds : angle 3.99018 ( 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 197 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.302 Fit side-chains REVERT: A 218 GLU cc_start: 0.8514 (tp30) cc_final: 0.8093 (tp30) REVERT: A 323 TYR cc_start: 0.9116 (t80) cc_final: 0.8893 (t80) REVERT: A 362 ARG cc_start: 0.5313 (ptt90) cc_final: 0.4386 (ptt90) REVERT: A 383 GLN cc_start: 0.9038 (mt0) cc_final: 0.8532 (mt0) REVERT: A 390 LYS cc_start: 0.9562 (tmtt) cc_final: 0.8663 (mptt) REVERT: A 431 ASP cc_start: 0.8817 (m-30) cc_final: 0.8142 (m-30) REVERT: B 218 GLU cc_start: 0.8670 (tp30) cc_final: 0.8441 (mm-30) REVERT: B 323 TYR cc_start: 0.9353 (t80) cc_final: 0.9122 (t80) REVERT: B 374 LYS cc_start: 0.8081 (mptt) cc_final: 0.7871 (mptt) REVERT: B 378 HIS cc_start: 0.9015 (m-70) cc_final: 0.8603 (m90) REVERT: B 383 GLN cc_start: 0.8880 (mt0) cc_final: 0.8283 (mt0) REVERT: B 390 LYS cc_start: 0.9520 (tmtt) cc_final: 0.8629 (mptt) REVERT: B 441 THR cc_start: 0.8963 (m) cc_final: 0.8621 (t) REVERT: C 383 GLN cc_start: 0.8737 (mt0) cc_final: 0.8036 (mp10) REVERT: C 390 LYS cc_start: 0.9336 (tmtt) cc_final: 0.8376 (mptt) REVERT: C 431 ASP cc_start: 0.8887 (m-30) cc_final: 0.8229 (m-30) REVERT: D 218 GLU cc_start: 0.8591 (tp30) cc_final: 0.8214 (tp30) REVERT: D 293 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8787 (tm-30) REVERT: D 362 ARG cc_start: 0.5129 (ptt90) cc_final: 0.4444 (ptt180) REVERT: D 383 GLN cc_start: 0.8656 (mt0) cc_final: 0.8115 (mp10) REVERT: D 390 LYS cc_start: 0.9537 (tmtt) cc_final: 0.8655 (mptt) REVERT: D 431 ASP cc_start: 0.8868 (m-30) cc_final: 0.8195 (m-30) REVERT: D 481 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (t80) outliers start: 39 outliers final: 23 residues processed: 188 average time/residue: 0.0723 time to fit residues: 18.5490 Evaluate side-chains 168 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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 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 481 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079401 restraints weight = 18431.972| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.12 r_work: 0.3074 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7792 Z= 0.115 Angle : 0.519 5.944 10596 Z= 0.271 Chirality : 0.039 0.205 1268 Planarity : 0.003 0.028 1268 Dihedral : 6.363 57.853 1036 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.07 % Allowed : 22.25 % Favored : 73.68 % 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: 1.34 (0.28), residues: 920 helix: 1.28 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 394 TYR 0.011 0.001 TYR D 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 covalent geometry : bond 0.00251 ( 7792) covalent geometry : angle 0.51942 (10596) hydrogen bonds : bond 0.03765 ( 502) hydrogen bonds : angle 3.86303 ( 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 188 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.179 Fit side-chains REVERT: A 218 GLU cc_start: 0.8627 (tp30) cc_final: 0.8150 (tp30) REVERT: A 362 ARG cc_start: 0.5019 (ptt90) cc_final: 0.3850 (ptt90) REVERT: A 380 LYS cc_start: 0.8919 (mppt) cc_final: 0.8664 (mppt) REVERT: A 383 GLN cc_start: 0.8951 (mt0) cc_final: 0.8419 (mt0) REVERT: A 390 LYS cc_start: 0.9506 (tmtt) cc_final: 0.8613 (mptt) REVERT: A 431 ASP cc_start: 0.8903 (m-30) cc_final: 0.8201 (m-30) REVERT: A 481 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8644 (t80) REVERT: B 218 GLU cc_start: 0.8805 (tp30) cc_final: 0.8539 (mm-30) REVERT: B 383 GLN cc_start: 0.8882 (mt0) cc_final: 0.8255 (mt0) REVERT: B 390 LYS cc_start: 0.9437 (tmtt) cc_final: 0.8511 (mptt) REVERT: C 323 TYR cc_start: 0.9309 (t80) cc_final: 0.8906 (t80) REVERT: C 383 GLN cc_start: 0.8734 (mt0) cc_final: 0.8049 (mp10) REVERT: C 390 LYS cc_start: 0.9298 (tmtt) cc_final: 0.8318 (mptt) REVERT: C 395 GLU cc_start: 0.8557 (mp0) cc_final: 0.8354 (mp0) REVERT: C 431 ASP cc_start: 0.8934 (m-30) cc_final: 0.8243 (m-30) REVERT: D 218 GLU cc_start: 0.8693 (tp30) cc_final: 0.8357 (tp30) REVERT: D 293 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8744 (tm-30) REVERT: D 362 ARG cc_start: 0.4935 (ptt90) cc_final: 0.3451 (ptt90) REVERT: D 383 GLN cc_start: 0.8651 (mt0) cc_final: 0.8098 (mp10) REVERT: D 390 LYS cc_start: 0.9526 (tmtt) cc_final: 0.8620 (mptt) REVERT: D 431 ASP cc_start: 0.8937 (m-30) cc_final: 0.8259 (m-30) REVERT: D 485 TYR cc_start: 0.6360 (m-80) cc_final: 0.6057 (m-80) outliers start: 34 outliers final: 26 residues processed: 174 average time/residue: 0.0748 time to fit residues: 17.7204 Evaluate side-chains 173 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 407 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 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 470 ILE Chi-restraints excluded: chain C residue 228 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 467 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 407 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075378 restraints weight = 18742.298| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.21 r_work: 0.3064 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7792 Z= 0.119 Angle : 0.521 5.634 10596 Z= 0.272 Chirality : 0.038 0.141 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.746 58.187 1028 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.90 % Allowed : 22.37 % Favored : 72.73 % 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: 1.40 (0.28), residues: 920 helix: 1.32 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 384 TYR 0.022 0.001 TYR B 323 PHE 0.008 0.001 PHE C 410 TRP 0.007 0.001 TRP D 435 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7792) covalent geometry : angle 0.52056 (10596) hydrogen bonds : bond 0.03647 ( 502) hydrogen bonds : angle 3.81888 ( 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 197 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.203 Fit side-chains REVERT: A 218 GLU cc_start: 0.8581 (tp30) cc_final: 0.8095 (tp30) REVERT: A 362 ARG cc_start: 0.5040 (ptt90) cc_final: 0.3843 (ptt90) REVERT: A 390 LYS cc_start: 0.9480 (tmtt) cc_final: 0.8539 (mptt) REVERT: A 431 ASP cc_start: 0.8897 (m-30) cc_final: 0.8198 (m-30) REVERT: A 481 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8658 (t80) REVERT: B 218 GLU cc_start: 0.8810 (tp30) cc_final: 0.8487 (tp30) REVERT: B 380 LYS cc_start: 0.8889 (mppt) cc_final: 0.8638 (mppt) REVERT: B 383 GLN cc_start: 0.8839 (mt0) cc_final: 0.8211 (mt0) REVERT: B 390 LYS cc_start: 0.9442 (tmtt) cc_final: 0.8513 (mptt) REVERT: C 323 TYR cc_start: 0.9387 (t80) cc_final: 0.9030 (t80) REVERT: C 383 GLN cc_start: 0.8731 (mt0) cc_final: 0.8056 (mp10) REVERT: C 390 LYS cc_start: 0.9349 (tmtt) cc_final: 0.8364 (mptt) REVERT: C 431 ASP cc_start: 0.8947 (m-30) cc_final: 0.8275 (m-30) REVERT: D 218 GLU cc_start: 0.8694 (tp30) cc_final: 0.8369 (tp30) REVERT: D 293 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8754 (tm-30) REVERT: D 362 ARG cc_start: 0.5004 (ptt90) cc_final: 0.3763 (ptt180) REVERT: D 383 GLN cc_start: 0.8665 (mt0) cc_final: 0.8103 (mp10) REVERT: D 390 LYS cc_start: 0.9527 (tmtt) cc_final: 0.8623 (mptt) REVERT: D 431 ASP cc_start: 0.8935 (m-30) cc_final: 0.8265 (m-30) outliers start: 41 outliers final: 31 residues processed: 179 average time/residue: 0.0723 time to fit residues: 17.5203 Evaluate side-chains 180 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain A residue 407 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 228 VAL Chi-restraints excluded: chain B residue 241 ILE 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 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 D residue 228 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 407 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: 5.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 70 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084626 restraints weight = 18282.117| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.26 r_work: 0.3071 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1134 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= 0.120 Angle : 0.539 5.805 10596 Z= 0.280 Chirality : 0.038 0.140 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.637 58.612 1026 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.78 % Allowed : 23.80 % Favored : 71.41 % 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: 1.41 (0.28), residues: 920 helix: 1.33 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.48 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 384 TYR 0.026 0.001 TYR B 323 PHE 0.008 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 covalent geometry : bond 0.00269 ( 7792) covalent geometry : angle 0.53904 (10596) hydrogen bonds : bond 0.03557 ( 502) hydrogen bonds : angle 3.77419 ( 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 195 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.311 Fit side-chains REVERT: A 218 GLU cc_start: 0.8618 (tp30) cc_final: 0.8122 (tp30) REVERT: A 362 ARG cc_start: 0.4880 (ptt90) cc_final: 0.3702 (ptt90) REVERT: A 380 LYS cc_start: 0.8855 (mppt) cc_final: 0.8580 (mppt) REVERT: A 383 GLN cc_start: 0.8810 (mt0) cc_final: 0.8339 (mt0) REVERT: A 390 LYS cc_start: 0.9456 (tmtt) cc_final: 0.8503 (mptt) REVERT: A 431 ASP cc_start: 0.8926 (m-30) cc_final: 0.8197 (m-30) REVERT: B 218 GLU cc_start: 0.8840 (tp30) cc_final: 0.8499 (tp30) REVERT: B 380 LYS cc_start: 0.8904 (mppt) cc_final: 0.8633 (mppt) REVERT: B 383 GLN cc_start: 0.8806 (mt0) cc_final: 0.8164 (mt0) REVERT: B 390 LYS cc_start: 0.9415 (tmtt) cc_final: 0.8476 (mptt) REVERT: C 232 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 323 TYR cc_start: 0.9396 (t80) cc_final: 0.9058 (t80) REVERT: C 383 GLN cc_start: 0.8749 (mt0) cc_final: 0.8164 (mp10) REVERT: C 390 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8341 (mptt) REVERT: C 405 ILE cc_start: 0.9077 (tp) cc_final: 0.8790 (tp) REVERT: C 431 ASP cc_start: 0.8950 (m-30) cc_final: 0.8294 (m-30) REVERT: D 218 GLU cc_start: 0.8710 (tp30) cc_final: 0.8351 (tp30) REVERT: D 293 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 362 ARG cc_start: 0.4815 (ptt90) cc_final: 0.3585 (ptt180) REVERT: D 383 GLN cc_start: 0.8649 (mt0) cc_final: 0.8103 (mp10) REVERT: D 390 LYS cc_start: 0.9505 (tmtt) cc_final: 0.8611 (mptt) REVERT: D 431 ASP cc_start: 0.8951 (m-30) cc_final: 0.8248 (m-30) outliers start: 40 outliers final: 31 residues processed: 179 average time/residue: 0.0669 time to fit residues: 16.4970 Evaluate side-chains 183 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain A residue 399 LEU 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 243 ILE Chi-restraints excluded: chain B residue 312 MET 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 470 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 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 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: 1.9990 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085562 restraints weight = 18214.797| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.21 r_work: 0.3107 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7792 Z= 0.116 Angle : 0.539 6.350 10596 Z= 0.279 Chirality : 0.039 0.150 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.264 50.991 1023 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.07 % Allowed : 24.76 % Favored : 71.17 % 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: 1.44 (0.28), residues: 920 helix: 1.35 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 384 TYR 0.028 0.001 TYR B 323 PHE 0.008 0.001 PHE C 410 TRP 0.007 0.001 TRP D 435 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7792) covalent geometry : angle 0.53942 (10596) hydrogen bonds : bond 0.03496 ( 502) hydrogen bonds : angle 3.73794 ( 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 198 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.203 Fit side-chains REVERT: A 218 GLU cc_start: 0.8557 (tp30) cc_final: 0.8065 (tp30) REVERT: A 362 ARG cc_start: 0.4925 (ptt90) cc_final: 0.3732 (ptt90) REVERT: A 390 LYS cc_start: 0.9447 (tmtt) cc_final: 0.8467 (mmtt) REVERT: A 431 ASP cc_start: 0.8832 (m-30) cc_final: 0.8133 (m-30) REVERT: B 218 GLU cc_start: 0.8842 (tp30) cc_final: 0.8551 (mm-30) REVERT: B 390 LYS cc_start: 0.9417 (tmtt) cc_final: 0.8479 (mptt) REVERT: C 232 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (tt) REVERT: C 323 TYR cc_start: 0.9380 (t80) cc_final: 0.9090 (t80) REVERT: C 383 GLN cc_start: 0.8752 (mt0) cc_final: 0.8168 (mp10) REVERT: C 390 LYS cc_start: 0.9370 (tmtt) cc_final: 0.8418 (mptt) REVERT: C 405 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (tp) REVERT: C 431 ASP cc_start: 0.8919 (m-30) cc_final: 0.8273 (m-30) REVERT: D 218 GLU cc_start: 0.8646 (tp30) cc_final: 0.8300 (tp30) REVERT: D 293 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 362 ARG cc_start: 0.4922 (ptt90) cc_final: 0.3685 (ptt180) REVERT: D 383 GLN cc_start: 0.8649 (mt0) cc_final: 0.8130 (mp10) REVERT: D 390 LYS cc_start: 0.9512 (tmtt) cc_final: 0.8621 (mptt) REVERT: D 431 ASP cc_start: 0.8919 (m-30) cc_final: 0.8229 (m-30) outliers start: 34 outliers final: 28 residues processed: 182 average time/residue: 0.0663 time to fit residues: 16.6645 Evaluate side-chains 186 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain A residue 407 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 243 ILE Chi-restraints excluded: chain B residue 312 MET 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 470 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 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 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 228 VAL Chi-restraints excluded: chain D residue 407 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: 2.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087768 restraints weight = 18193.255| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.11 r_work: 0.3033 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 0.036 7792 Z= 0.151 Angle : 0.585 6.778 10596 Z= 0.303 Chirality : 0.039 0.156 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.252 50.924 1022 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.67 % Allowed : 24.40 % Favored : 70.93 % 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 : -0.50 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.030 0.002 TYR B 323 PHE 0.007 0.001 PHE A 373 TRP 0.007 0.001 TRP D 289 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7792) covalent geometry : angle 0.58510 (10596) hydrogen bonds : bond 0.03582 ( 502) hydrogen bonds : angle 3.80562 ( 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 190 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.253 Fit side-chains REVERT: A 218 GLU cc_start: 0.8577 (tp30) cc_final: 0.8115 (tp30) REVERT: A 362 ARG cc_start: 0.5022 (ptt90) cc_final: 0.3783 (ptt180) REVERT: A 383 GLN cc_start: 0.8871 (mt0) cc_final: 0.8446 (mt0) REVERT: A 390 LYS cc_start: 0.9465 (tmtt) cc_final: 0.8493 (mmtt) REVERT: A 431 ASP cc_start: 0.8907 (m-30) cc_final: 0.8179 (m-30) REVERT: B 218 GLU cc_start: 0.8878 (tp30) cc_final: 0.8598 (mm-30) REVERT: B 383 GLN cc_start: 0.8848 (mt0) cc_final: 0.8183 (mt0) REVERT: B 390 LYS cc_start: 0.9438 (tmtt) cc_final: 0.8518 (mptt) REVERT: B 441 THR cc_start: 0.8873 (m) cc_final: 0.8411 (t) REVERT: C 232 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (tt) REVERT: C 383 GLN cc_start: 0.8757 (mt0) cc_final: 0.8155 (mp10) REVERT: C 390 LYS cc_start: 0.9413 (tmtt) cc_final: 0.8496 (mptt) REVERT: C 405 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (tp) REVERT: C 431 ASP cc_start: 0.8972 (m-30) cc_final: 0.8307 (m-30) REVERT: D 218 GLU cc_start: 0.8612 (tp30) cc_final: 0.8255 (tp30) REVERT: D 293 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8774 (tm-30) REVERT: D 323 TYR cc_start: 0.9323 (t80) cc_final: 0.8831 (t80) REVERT: D 362 ARG cc_start: 0.5078 (ptt90) cc_final: 0.3760 (ptt180) REVERT: D 383 GLN cc_start: 0.8669 (mt0) cc_final: 0.8175 (mp10) REVERT: D 390 LYS cc_start: 0.9514 (tmtt) cc_final: 0.8659 (mptt) REVERT: D 431 ASP cc_start: 0.8991 (m-30) cc_final: 0.8311 (m-30) outliers start: 39 outliers final: 34 residues processed: 173 average time/residue: 0.0662 time to fit residues: 15.5157 Evaluate side-chains 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 228 VAL 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 C residue 228 VAL Chi-restraints excluded: chain C residue 232 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089341 restraints weight = 18738.770| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.41 r_work: 0.2938 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7792 Z= 0.129 Angle : 0.576 7.463 10596 Z= 0.299 Chirality : 0.039 0.154 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.219 50.918 1022 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.55 % Allowed : 25.72 % 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: 1.46 (0.28), residues: 920 helix: 1.38 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.030 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 covalent geometry : bond 0.00298 ( 7792) covalent geometry : angle 0.57609 (10596) hydrogen bonds : bond 0.03519 ( 502) hydrogen bonds : angle 3.76742 ( 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 196 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8661 (tp30) cc_final: 0.8211 (tp30) REVERT: A 323 TYR cc_start: 0.9242 (t80) cc_final: 0.9033 (t80) REVERT: A 362 ARG cc_start: 0.4659 (ptt90) cc_final: 0.3582 (ptt90) REVERT: A 383 GLN cc_start: 0.8784 (mt0) cc_final: 0.8330 (mt0) REVERT: A 390 LYS cc_start: 0.9406 (tmtt) cc_final: 0.8409 (mmtt) REVERT: A 431 ASP cc_start: 0.8912 (m-30) cc_final: 0.8205 (m-30) REVERT: B 218 GLU cc_start: 0.8895 (tp30) cc_final: 0.8604 (mm-30) REVERT: B 383 GLN cc_start: 0.8737 (mt0) cc_final: 0.8104 (mt0) REVERT: B 390 LYS cc_start: 0.9403 (tmtt) cc_final: 0.8454 (mptt) REVERT: C 232 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8681 (tt) REVERT: C 383 GLN cc_start: 0.8674 (mt0) cc_final: 0.8018 (mp10) REVERT: C 390 LYS cc_start: 0.9379 (tmtt) cc_final: 0.8449 (mptt) REVERT: C 405 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 431 ASP cc_start: 0.9012 (m-30) cc_final: 0.8366 (m-30) REVERT: D 218 GLU cc_start: 0.8653 (tp30) cc_final: 0.8318 (tp30) REVERT: D 293 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8681 (tm-30) REVERT: D 323 TYR cc_start: 0.9351 (t80) cc_final: 0.8895 (t80) REVERT: D 362 ARG cc_start: 0.4623 (ptt90) cc_final: 0.3463 (ptt180) REVERT: D 383 GLN cc_start: 0.8632 (mt0) cc_final: 0.8141 (mp10) REVERT: D 390 LYS cc_start: 0.9497 (tmtt) cc_final: 0.8619 (mptt) REVERT: D 431 ASP cc_start: 0.9053 (m-30) cc_final: 0.8374 (m-30) outliers start: 38 outliers final: 32 residues processed: 181 average time/residue: 0.0681 time to fit residues: 16.9411 Evaluate side-chains 187 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 467 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 241 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 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 C residue 228 VAL Chi-restraints excluded: chain C residue 232 ILE 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 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 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: 0.4980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 0.0010 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090128 restraints weight = 18720.936| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.47 r_work: 0.2968 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.042 7792 Z= 0.125 Angle : 0.610 8.039 10596 Z= 0.313 Chirality : 0.039 0.159 1268 Planarity : 0.003 0.029 1268 Dihedral : 5.132 51.159 1020 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.35 % Allowed : 27.27 % Favored : 69.38 % 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: 1.37 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 371 TYR 0.029 0.001 TYR B 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 covalent geometry : bond 0.00281 ( 7792) covalent geometry : angle 0.61049 (10596) hydrogen bonds : bond 0.03410 ( 502) hydrogen bonds : angle 3.72225 ( 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 188 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.244 Fit side-chains REVERT: A 218 GLU cc_start: 0.8642 (tp30) cc_final: 0.8170 (tp30) REVERT: A 323 TYR cc_start: 0.9273 (t80) cc_final: 0.8966 (t80) REVERT: A 362 ARG cc_start: 0.4451 (ptt90) cc_final: 0.3434 (ptt90) REVERT: A 383 GLN cc_start: 0.8803 (mt0) cc_final: 0.8339 (mt0) REVERT: A 390 LYS cc_start: 0.9408 (tmtt) cc_final: 0.8388 (mmtt) REVERT: A 431 ASP cc_start: 0.8885 (m-30) cc_final: 0.8208 (m-30) REVERT: B 218 GLU cc_start: 0.8877 (tp30) cc_final: 0.8572 (mm-30) REVERT: B 323 TYR cc_start: 0.9374 (t80) cc_final: 0.9165 (t80) REVERT: B 383 GLN cc_start: 0.8724 (mt0) cc_final: 0.8065 (mt0) REVERT: B 390 LYS cc_start: 0.9384 (tmtt) cc_final: 0.8448 (mptt) REVERT: B 441 THR cc_start: 0.8809 (m) cc_final: 0.8442 (t) REVERT: C 232 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 383 GLN cc_start: 0.8657 (mt0) cc_final: 0.8020 (mp10) REVERT: C 390 LYS cc_start: 0.9321 (tmtt) cc_final: 0.8384 (mptt) REVERT: C 431 ASP cc_start: 0.8986 (m-30) cc_final: 0.8358 (m-30) REVERT: D 218 GLU cc_start: 0.8626 (tp30) cc_final: 0.8281 (tp30) REVERT: D 293 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8659 (tm-30) REVERT: D 323 TYR cc_start: 0.9327 (t80) cc_final: 0.8861 (t80) REVERT: D 362 ARG cc_start: 0.4504 (ptt90) cc_final: 0.3416 (ptt180) REVERT: D 383 GLN cc_start: 0.8639 (mt0) cc_final: 0.8125 (mp10) REVERT: D 390 LYS cc_start: 0.9486 (tmtt) cc_final: 0.8593 (mptt) REVERT: D 431 ASP cc_start: 0.9012 (m-30) cc_final: 0.8312 (m-30) outliers start: 28 outliers final: 22 residues processed: 178 average time/residue: 0.0664 time to fit residues: 16.1844 Evaluate side-chains 178 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 407 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 C residue 232 ILE Chi-restraints excluded: chain C residue 243 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 407 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070265 restraints weight = 18769.472| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.24 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: 0.7788 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 7792 Z= 0.140 Angle : 0.623 8.119 10596 Z= 0.318 Chirality : 0.040 0.171 1268 Planarity : 0.003 0.028 1268 Dihedral : 5.155 50.702 1020 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.23 % Allowed : 26.91 % Favored : 69.86 % 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: 1.37 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 368 TYR 0.029 0.001 TYR B 323 PHE 0.008 0.001 PHE C 404 TRP 0.008 0.001 TRP C 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7792) covalent geometry : angle 0.62332 (10596) hydrogen bonds : bond 0.03521 ( 502) hydrogen bonds : angle 3.72136 ( 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 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8675 (tp30) cc_final: 0.8149 (tp30) REVERT: A 323 TYR cc_start: 0.9257 (t80) cc_final: 0.8909 (t80) REVERT: A 362 ARG cc_start: 0.4044 (ptt90) cc_final: 0.3095 (ptt90) REVERT: A 383 GLN cc_start: 0.8742 (mt0) cc_final: 0.8288 (mt0) REVERT: A 390 LYS cc_start: 0.9352 (tmtt) cc_final: 0.8364 (mmtt) REVERT: A 431 ASP cc_start: 0.8913 (m-30) cc_final: 0.8230 (m-30) REVERT: B 218 GLU cc_start: 0.8868 (tp30) cc_final: 0.8571 (mm-30) REVERT: B 323 TYR cc_start: 0.9329 (t80) cc_final: 0.9011 (t80) REVERT: B 383 GLN cc_start: 0.8667 (mt0) cc_final: 0.8218 (mt0) REVERT: B 390 LYS cc_start: 0.9354 (tmtt) cc_final: 0.8386 (mptt) REVERT: B 441 THR cc_start: 0.8680 (m) cc_final: 0.8295 (t) REVERT: C 383 GLN cc_start: 0.8583 (mt0) cc_final: 0.7949 (mp10) REVERT: C 390 LYS cc_start: 0.9294 (tmtt) cc_final: 0.8425 (mptt) REVERT: C 431 ASP cc_start: 0.8973 (m-30) cc_final: 0.8319 (m-30) REVERT: D 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8342 (tp30) REVERT: D 293 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8547 (tm-30) REVERT: D 323 TYR cc_start: 0.9231 (t80) cc_final: 0.8782 (t80) REVERT: D 362 ARG cc_start: 0.4016 (ptt90) cc_final: 0.3052 (ptt180) REVERT: D 383 GLN cc_start: 0.8552 (mt0) cc_final: 0.8033 (mp10) REVERT: D 390 LYS cc_start: 0.9438 (tmtt) cc_final: 0.8550 (mptt) REVERT: D 431 ASP cc_start: 0.9023 (m-30) cc_final: 0.8309 (m-30) outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 0.0675 time to fit residues: 15.5252 Evaluate side-chains 177 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 407 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 C residue 243 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 400 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 0.0010 chunk 24 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090051 restraints weight = 18732.549| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.48 r_work: 0.2967 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 7792 Z= 0.133 Angle : 0.627 8.085 10596 Z= 0.321 Chirality : 0.039 0.165 1268 Planarity : 0.003 0.029 1268 Dihedral : 5.177 51.218 1020 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 27.27 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.28), residues: 920 helix: 1.37 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 371 TYR 0.029 0.001 TYR B 323 PHE 0.008 0.001 PHE D 410 TRP 0.008 0.001 TRP C 435 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7792) covalent geometry : angle 0.62729 (10596) hydrogen bonds : bond 0.03439 ( 502) hydrogen bonds : angle 3.68425 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1349.79 seconds wall clock time: 23 minutes 51.65 seconds (1431.65 seconds total)