Starting phenix.real_space_refine on Fri Oct 23 05:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9www_66323/10_2026/9www_66323.map" } resolution = 3.81 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= 0.013 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 P 6 5.49 5 S 56 5.16 5 C 5511 2.51 5 N 1396 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8477 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3372 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3351 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8477 At special positions: 0 Unit cell: (101.504, 65.728, 97.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 6 15.00 O 1508 8.00 N 1396 7.00 C 5511 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 223.9 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 3 sheets defined 74.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 26 through 51 removed outlier: 4.327A pdb=" N ARG A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.615A pdb=" N GLY A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 109 Processing helix chain 'A' and resid 114 through 147 Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.643A pdb=" N ASN A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.648A pdb=" N HIS A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 236 removed outlier: 3.581A pdb=" N VAL A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.573A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.860A pdb=" N ARG A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.706A pdb=" N PHE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.951A pdb=" N LEU A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 26 through 50 removed outlier: 3.577A pdb=" N ARG B 31 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 78 Processing helix chain 'B' and resid 82 through 108 removed outlier: 3.569A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 146 removed outlier: 3.821A pdb=" N VAL B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 181 Processing helix chain 'B' and resid 183 through 208 removed outlier: 5.220A pdb=" N MET B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 237 Processing helix chain 'B' and resid 238 through 263 removed outlier: 4.025A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 336 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'C' and resid 405 through 419 Processing helix chain 'C' and resid 421 through 445 removed outlier: 3.705A pdb=" N LEU C 425 " --> pdb=" O PRO C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 462 Processing helix chain 'C' and resid 464 through 475 removed outlier: 3.847A pdb=" N ALA C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY C 475 " --> pdb=" O GLN C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 507 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 421 through 445 Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 464 through 474 removed outlier: 3.942A pdb=" N GLN D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 508 Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.765A pdb=" N VAL A 387 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 369 through 371 removed outlier: 8.035A pdb=" N LEU B 370 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE B 342 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 309 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY B 343 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE B 311 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 308 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU B 386 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 310 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE B 388 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR B 312 " --> pdb=" O ILE B 388 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1815 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: 1.24 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2612 1.33 - 1.45: 1596 1.45 - 1.57: 4333 1.57 - 1.69: 10 1.69 - 1.81: 106 Bond restraints: 8657 Sorted by residual: bond pdb=" O2B NDP B 501 " pdb=" P2B NDP B 501 " ideal model delta sigma weight residual 1.833 1.600 0.233 3.80e-02 6.93e+02 3.76e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.604 0.229 3.80e-02 6.93e+02 3.64e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.608 0.149 3.50e-02 8.16e+02 1.81e+01 bond pdb=" CA SER B 152 " pdb=" C SER B 152 " ideal model delta sigma weight residual 1.531 1.508 0.023 5.40e-03 3.43e+04 1.76e+01 bond pdb=" O5D NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 1.757 1.612 0.145 3.50e-02 8.16e+02 1.72e+01 ... (remaining 8652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 11492 3.61 - 7.21: 258 7.21 - 10.82: 27 10.82 - 14.43: 4 14.43 - 18.03: 3 Bond angle restraints: 11784 Sorted by residual: angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 111.28 101.04 10.24 1.09e+00 8.42e-01 8.82e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.96 -16.12 1.91e+00 2.73e-01 7.09e+01 angle pdb=" N PHE D 483 " pdb=" CA PHE D 483 " pdb=" C PHE D 483 " ideal model delta sigma weight residual 111.14 102.85 8.29 1.08e+00 8.57e-01 5.90e+01 angle pdb=" N HIS B 307 " pdb=" CA HIS B 307 " pdb=" C HIS B 307 " ideal model delta sigma weight residual 114.09 102.73 11.36 1.55e+00 4.16e-01 5.37e+01 angle pdb=" C5B NDP B 501 " pdb=" O5B NDP B 501 " pdb=" PA NDP B 501 " ideal model delta sigma weight residual 103.84 116.97 -13.13 1.91e+00 2.73e-01 4.70e+01 ... (remaining 11779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 4533 35.32 - 70.64: 452 70.64 - 105.96: 19 105.96 - 141.28: 0 141.28 - 176.60: 2 Dihedral angle restraints: 5006 sinusoidal: 1841 harmonic: 3165 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 -1.56 176.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5B NDP B 501 " pdb=" O5B NDP B 501 " pdb=" PA NDP B 501 " pdb=" O3 NDP B 501 " ideal model delta sinusoidal sigma weight residual 175.04 -22.13 -162.83 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA ASP B 373 " pdb=" CB ASP B 373 " pdb=" CG ASP B 373 " pdb=" OD1 ASP B 373 " ideal model delta sinusoidal sigma weight residual -30.00 -89.48 59.48 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 5003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1049 0.050 - 0.100: 276 0.100 - 0.149: 74 0.149 - 0.199: 16 0.199 - 0.249: 2 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C4D NDP B 501 " pdb=" C3D NDP B 501 " pdb=" C5D NDP B 501 " pdb=" O4D NDP B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.47 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3B NDP B 501 " pdb=" C2B NDP B 501 " pdb=" C4B NDP B 501 " pdb=" O3B NDP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 1414 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 153 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO B 154 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 436 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 437 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 346 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.020 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 13 1.94 - 2.68: 1268 2.68 - 3.42: 16558 3.42 - 4.16: 24482 4.16 - 4.90: 40367 Nonbonded interactions: 82688 Sorted by model distance: nonbonded pdb=" O LEU B 205 " pdb=" N ALA B 207 " model vdw 1.203 3.120 nonbonded pdb=" OE2 GLU A 287 " pdb=" C GLY A 289 " model vdw 1.204 3.270 nonbonded pdb=" NZ LYS D 509 " pdb=" OD1 ASN D 510 " model vdw 1.262 3.120 nonbonded pdb=" OE1 GLU A 287 " pdb=" CA HIS A 291 " model vdw 1.366 3.470 nonbonded pdb=" OE1 GLU A 287 " pdb=" N HIS A 291 " model vdw 1.375 3.120 ... (remaining 82683 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 1 through 277 or resid 287 or resid 291 through 501)) selection = (chain 'B' and (resid 1 through 277 or resid 290 through 501)) } ncs_group { reference = 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 group one per residue 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: 1.530 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.030 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.012 0.247 8658 Z= 0.836 Angle : 1.337 18.034 11784 Z= 0.834 Chirality : 0.051 0.249 1417 Planarity : 0.004 0.062 1458 Dihedral : 23.656 176.603 2978 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 75.45 Ramachandran Plot: Outliers : 9.02 % Allowed : 37.15 % Favored : 53.83 % Rotamer: Outliers : 37.13 % Allowed : 17.88 % Favored : 44.99 % 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: -8.36 (0.11), residues: 1109 helix: -5.22 (0.06), residues: 730 sheet: -4.37 (0.55), residues: 50 loop : -5.91 (0.20), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.016 0.002 TYR B 366 PHE 0.022 0.001 PHE B 440 TRP 0.018 0.002 TRP A 415 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.01170 / 0.79 ( 8657) covalent geometry : angle 1.33659 / 0.83 (11784) hydrogen bonds : bond 0.23672 / 16.07 ( 615) hydrogen bonds : angle 11.29517 / 7.80 ( 1815) Misc. bond : bond 0.24682 / 12.99 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 441 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.9066 (mt) cc_final: 0.8697 (mp) REVERT: A 361 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: A 411 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (m) REVERT: A 439 PHE cc_start: 0.8429 (m-10) cc_final: 0.7950 (m-80) REVERT: A 444 THR cc_start: 0.8945 (m) cc_final: 0.8497 (t) REVERT: B 35 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 90 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7678 (tp) REVERT: B 116 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7969 (tt) REVERT: B 121 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7721 (t-170) REVERT: B 154 PRO cc_start: 0.7472 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: B 156 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6300 (tmm) REVERT: B 194 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5148 (mtm) REVERT: B 214 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8482 (mmp) REVERT: B 221 LEU cc_start: 0.9437 (mt) cc_final: 0.9159 (mt) REVERT: B 268 ILE cc_start: 0.8732 (mp) cc_final: 0.8514 (mm) REVERT: B 294 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 372 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5205 (tmm) REVERT: B 395 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7674 (t0) REVERT: B 414 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8440 (m) REVERT: B 456 ASP cc_start: 0.7976 (m-30) cc_final: 0.7774 (t0) REVERT: B 459 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7768 (mt) REVERT: C 406 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: C 412 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8625 (tp) REVERT: C 413 PHE cc_start: 0.8508 (t80) cc_final: 0.8234 (t80) REVERT: C 419 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 472 ILE cc_start: 0.9138 (tt) cc_final: 0.8764 (tt) REVERT: C 500 THR cc_start: 0.9228 (m) cc_final: 0.8391 (m) REVERT: C 502 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: C 506 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8246 (mtp) REVERT: D 429 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9318 (m) REVERT: D 461 SER cc_start: 0.9388 (p) cc_final: 0.9168 (p) outliers start: 326 outliers final: 111 residues processed: 581 average time/residue: 0.0841 time to fit residues: 67.6945 Evaluate side-chains 437 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 306 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 415 TRP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 509 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 164 ASN A 305 ASN A 419 ASN B 27 HIS B 34 ASN B 108 HIS B 109 HIS B 164 ASN B 187 GLN B 204 HIS B 428 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN D 427 HIS D 444 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095945 restraints weight = 20609.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098874 restraints weight = 10809.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100802 restraints weight = 6874.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102064 restraints weight = 5036.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102640 restraints weight = 4078.446| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8658 Z= 0.210 Angle : 0.926 7.670 11784 Z= 0.481 Chirality : 0.048 0.225 1417 Planarity : 0.007 0.067 1458 Dihedral : 15.344 165.877 1444 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.99 % Allowed : 11.63 % Favored : 87.38 % Rotamer: Outliers : 12.41 % Allowed : 24.37 % Favored : 63.21 % 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: -4.62 (0.20), residues: 1109 helix: -2.32 (0.15), residues: 771 sheet: -3.98 (0.54), residues: 54 loop : -4.49 (0.28), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.028 0.002 TYR A 366 PHE 0.039 0.003 PHE D 480 TRP 0.036 0.002 TRP B 415 HIS 0.027 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 8657) covalent geometry : angle 0.92607 / 0.48 (11784) hydrogen bonds : bond 0.06347 / 4.28 ( 615) hydrogen bonds : angle 6.11781 / 4.30 ( 1815) Misc. bond : bond 0.00312 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 375 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 SER cc_start: 0.4325 (OUTLIER) cc_final: 0.4060 (p) REVERT: A 19 PHE cc_start: 0.8881 (m-80) cc_final: 0.8375 (m-80) REVERT: A 26 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8160 (mmmt) REVERT: A 38 ILE cc_start: 0.9221 (mt) cc_final: 0.8888 (tp) REVERT: A 80 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.4767 (tpp) REVERT: A 172 PHE cc_start: 0.8917 (t80) cc_final: 0.8678 (t80) REVERT: A 187 GLN cc_start: 0.8952 (mt0) cc_final: 0.8647 (mp10) REVERT: A 291 HIS cc_start: 0.5499 (m-70) cc_final: 0.4946 (m-70) REVERT: A 334 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8148 (mtp85) REVERT: A 351 LEU cc_start: 0.8892 (tp) cc_final: 0.8658 (tt) REVERT: A 361 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: A 418 GLN cc_start: 0.7645 (mp10) cc_final: 0.7437 (mp10) REVERT: A 424 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7596 (ttpt) REVERT: A 444 THR cc_start: 0.8897 (m) cc_final: 0.8568 (p) REVERT: B 90 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 120 ILE cc_start: 0.8385 (mt) cc_final: 0.8088 (mm) REVERT: B 121 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8330 (t-170) REVERT: B 124 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 156 MET cc_start: 0.7360 (tpp) cc_final: 0.5726 (tmm) REVERT: B 214 MET cc_start: 0.9035 (mmp) cc_final: 0.8784 (mmm) REVERT: B 257 TYR cc_start: 0.8725 (t80) cc_final: 0.8481 (t80) REVERT: B 268 ILE cc_start: 0.8528 (mp) cc_final: 0.8296 (tt) REVERT: B 379 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: B 395 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 399 GLN cc_start: 0.7071 (mt0) cc_final: 0.6712 (mt0) REVERT: B 424 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5667 (tttt) REVERT: B 427 MET cc_start: 0.5397 (tpt) cc_final: 0.4684 (tpt) REVERT: B 450 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6573 (p0) REVERT: B 456 ASP cc_start: 0.8288 (m-30) cc_final: 0.8040 (t70) REVERT: C 406 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7152 (mtt) REVERT: C 412 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8229 (tp) REVERT: C 423 GLU cc_start: 0.8566 (mp0) cc_final: 0.8249 (mp0) REVERT: C 472 ILE cc_start: 0.9417 (tt) cc_final: 0.9172 (tt) REVERT: D 408 LEU cc_start: 0.8729 (mt) cc_final: 0.8509 (pp) REVERT: D 439 TYR cc_start: 0.8432 (t80) cc_final: 0.8164 (t80) REVERT: D 483 PHE cc_start: 0.8743 (t80) cc_final: 0.8323 (t80) REVERT: D 502 ARG cc_start: 0.9109 (ttm170) cc_final: 0.8857 (ttm-80) outliers start: 109 outliers final: 52 residues processed: 433 average time/residue: 0.0708 time to fit residues: 44.6120 Evaluate side-chains 373 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 309 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [101, 97, 102, 82, 54, 18, 40, 9, 16, 29, 67] chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 164 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 399 GLN B 27 HIS B 164 ASN B 187 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094230 restraints weight = 20828.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096944 restraints weight = 11054.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098736 restraints weight = 7173.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099806 restraints weight = 5370.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100630 restraints weight = 4498.207| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8658 Z= 0.201 Angle : 0.833 9.930 11784 Z= 0.428 Chirality : 0.047 0.243 1417 Planarity : 0.006 0.065 1458 Dihedral : 12.223 160.398 1286 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.38 % Favored : 89.81 % Rotamer: Outliers : 9.68 % Allowed : 25.17 % Favored : 65.15 % 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: -1.52 (0.24), residues: 1109 helix: 0.10 (0.18), residues: 770 sheet: -3.42 (0.54), residues: 58 loop : -3.50 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 265 TYR 0.022 0.002 TYR B 106 PHE 0.046 0.002 PHE D 480 TRP 0.015 0.001 TRP B 415 HIS 0.014 0.002 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 8657) covalent geometry : angle 0.83301 / 0.43 (11784) hydrogen bonds : bond 0.05521 / 3.74 ( 615) hydrogen bonds : angle 5.57143 / 3.96 ( 1815) Misc. bond : bond 0.00134 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8968 (m-80) cc_final: 0.8390 (m-80) REVERT: A 26 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8218 (mmmt) REVERT: A 38 ILE cc_start: 0.9242 (mt) cc_final: 0.8949 (tp) REVERT: A 172 PHE cc_start: 0.8953 (t80) cc_final: 0.8706 (t80) REVERT: A 187 GLN cc_start: 0.8865 (mt0) cc_final: 0.8580 (mp10) REVERT: A 254 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9306 (mp) REVERT: A 351 LEU cc_start: 0.9007 (tp) cc_final: 0.8757 (tt) REVERT: A 399 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7526 (mm110) REVERT: A 418 GLN cc_start: 0.7853 (mp10) cc_final: 0.7523 (mp10) REVERT: A 444 THR cc_start: 0.8920 (m) cc_final: 0.8593 (p) REVERT: B 61 LEU cc_start: 0.8883 (mt) cc_final: 0.8678 (mm) REVERT: B 80 MET cc_start: 0.8049 (mmm) cc_final: 0.7819 (mmm) REVERT: B 82 GLU cc_start: 0.8723 (pm20) cc_final: 0.8476 (pm20) REVERT: B 90 LEU cc_start: 0.9099 (mt) cc_final: 0.8890 (mt) REVERT: B 120 ILE cc_start: 0.8357 (mt) cc_final: 0.7961 (mm) REVERT: B 124 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 254 ILE cc_start: 0.9249 (mm) cc_final: 0.8777 (mm) REVERT: B 257 TYR cc_start: 0.8733 (t80) cc_final: 0.8517 (t80) REVERT: B 268 ILE cc_start: 0.8496 (mp) cc_final: 0.8286 (tt) REVERT: B 294 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7335 (tp) REVERT: B 298 GLU cc_start: 0.8721 (mp0) cc_final: 0.8395 (mp0) REVERT: B 305 ASN cc_start: 0.9201 (m110) cc_final: 0.8929 (p0) REVERT: B 317 MET cc_start: 0.8982 (tmm) cc_final: 0.8101 (tpt) REVERT: B 321 GLN cc_start: 0.7894 (tt0) cc_final: 0.7464 (pp30) REVERT: B 341 ARG cc_start: 0.5796 (mtm-85) cc_final: 0.5256 (ttm170) REVERT: B 395 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8072 (t0) REVERT: B 399 GLN cc_start: 0.7156 (mt0) cc_final: 0.6751 (mt0) REVERT: B 419 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6820 (t0) REVERT: B 421 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8801 (mt) REVERT: B 441 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8256 (mtpp) REVERT: B 456 ASP cc_start: 0.8361 (m-30) cc_final: 0.8088 (t70) REVERT: C 406 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.6932 (mtt) REVERT: C 412 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8290 (tp) REVERT: C 423 GLU cc_start: 0.8648 (mp0) cc_final: 0.8255 (mp0) REVERT: D 439 TYR cc_start: 0.8580 (t80) cc_final: 0.8370 (t80) REVERT: D 449 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9210 (mt) REVERT: D 483 PHE cc_start: 0.8717 (t80) cc_final: 0.8411 (t80) REVERT: D 491 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7507 (mp) REVERT: D 493 ILE cc_start: 0.9109 (mt) cc_final: 0.8875 (mt) REVERT: D 502 ARG cc_start: 0.9101 (ttm170) cc_final: 0.8782 (ttm-80) outliers start: 85 outliers final: 48 residues processed: 379 average time/residue: 0.0733 time to fit residues: 40.5928 Evaluate side-chains 356 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [30, 21, 12, 97, 52, 45, 102, 74, 108, 58, 39] chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 204 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 428 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.095511 restraints weight = 21043.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098340 restraints weight = 11112.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100067 restraints weight = 7150.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101307 restraints weight = 5382.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102098 restraints weight = 4451.914| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8658 Z= 0.174 Angle : 0.808 11.246 11784 Z= 0.405 Chirality : 0.046 0.313 1417 Planarity : 0.005 0.072 1458 Dihedral : 11.373 164.639 1253 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.84 % Favored : 91.43 % Rotamer: Outliers : 8.43 % Allowed : 27.56 % Favored : 64.01 % 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: 0.05 (0.25), residues: 1109 helix: 1.18 (0.18), residues: 777 sheet: -3.05 (0.60), residues: 59 loop : -2.59 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 425 TYR 0.027 0.002 TYR B 431 PHE 0.035 0.002 PHE D 480 TRP 0.011 0.001 TRP D 443 HIS 0.011 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 8657) covalent geometry : angle 0.80789 / 0.40 (11784) hydrogen bonds : bond 0.04998 / 3.34 ( 615) hydrogen bonds : angle 5.22616 / 3.73 ( 1815) Misc. bond : bond 0.00114 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 321 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8967 (m-80) cc_final: 0.8266 (m-80) REVERT: A 26 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8212 (mmmt) REVERT: A 38 ILE cc_start: 0.9253 (mt) cc_final: 0.9013 (tp) REVERT: A 43 ILE cc_start: 0.8715 (mt) cc_final: 0.8403 (mm) REVERT: A 187 GLN cc_start: 0.8783 (mt0) cc_final: 0.8558 (mt0) REVERT: A 214 MET cc_start: 0.9058 (mmm) cc_final: 0.8834 (mmm) REVERT: A 351 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 418 GLN cc_start: 0.7955 (mp10) cc_final: 0.7573 (mp10) REVERT: A 444 THR cc_start: 0.8920 (m) cc_final: 0.8704 (p) REVERT: B 35 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7753 (t0) REVERT: B 82 GLU cc_start: 0.8731 (pm20) cc_final: 0.8375 (pm20) REVERT: B 90 LEU cc_start: 0.9082 (mt) cc_final: 0.8829 (mt) REVERT: B 120 ILE cc_start: 0.8425 (mt) cc_final: 0.8020 (mm) REVERT: B 121 HIS cc_start: 0.9038 (OUTLIER) cc_final: 0.8710 (t70) REVERT: B 124 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 134 VAL cc_start: 0.9580 (t) cc_final: 0.9372 (m) REVERT: B 156 MET cc_start: 0.7277 (tpp) cc_final: 0.5929 (tmm) REVERT: B 263 MET cc_start: 0.8777 (tpt) cc_final: 0.8269 (tpp) REVERT: B 294 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7252 (tp) REVERT: B 298 GLU cc_start: 0.8745 (mp0) cc_final: 0.8449 (mp0) REVERT: B 317 MET cc_start: 0.8792 (tmm) cc_final: 0.8046 (tpt) REVERT: B 321 GLN cc_start: 0.7907 (tt0) cc_final: 0.7369 (pp30) REVERT: B 331 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8196 (tt0) REVERT: B 341 ARG cc_start: 0.5944 (mtm-85) cc_final: 0.5202 (ttp-110) REVERT: B 350 ARG cc_start: 0.7765 (mtm110) cc_final: 0.7544 (mtp180) REVERT: B 355 MET cc_start: 0.8409 (mmt) cc_final: 0.8208 (tpp) REVERT: B 379 PHE cc_start: 0.8212 (m-80) cc_final: 0.7494 (m-10) REVERT: B 395 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8104 (t0) REVERT: B 399 GLN cc_start: 0.7220 (mt0) cc_final: 0.7016 (mm-40) REVERT: B 421 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 456 ASP cc_start: 0.8477 (m-30) cc_final: 0.8268 (t70) REVERT: C 406 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7034 (mtp) REVERT: C 412 LEU cc_start: 0.8727 (mm) cc_final: 0.8214 (tp) REVERT: C 423 GLU cc_start: 0.8740 (mp0) cc_final: 0.8315 (mp0) REVERT: C 424 PHE cc_start: 0.8852 (t80) cc_final: 0.8604 (t80) REVERT: C 474 GLN cc_start: 0.8127 (mt0) cc_final: 0.7717 (mt0) REVERT: D 449 LEU cc_start: 0.9313 (mt) cc_final: 0.9053 (mt) REVERT: D 483 PHE cc_start: 0.8674 (t80) cc_final: 0.8457 (t80) REVERT: D 502 ARG cc_start: 0.9058 (ttm170) cc_final: 0.8757 (ttm170) outliers start: 74 outliers final: 44 residues processed: 361 average time/residue: 0.0726 time to fit residues: 37.8144 Evaluate side-chains 345 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [70, 95, 43, 22, 34, 6, 86, 19, 106, 17, 83] chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 35 ASN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 323 GLN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097630 restraints weight = 20494.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100537 restraints weight = 10722.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102440 restraints weight = 6891.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103680 restraints weight = 5097.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.104403 restraints weight = 4164.054| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8658 Z= 0.167 Angle : 0.802 13.733 11784 Z= 0.402 Chirality : 0.046 0.253 1417 Planarity : 0.005 0.073 1458 Dihedral : 10.759 166.585 1239 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.31 % Favored : 92.88 % Rotamer: Outliers : 7.18 % Allowed : 30.07 % Favored : 62.76 % 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: 0.59 (0.26), residues: 1109 helix: 1.61 (0.18), residues: 772 sheet: -2.52 (0.64), residues: 61 loop : -2.48 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 425 TYR 0.022 0.002 TYR B 106 PHE 0.023 0.002 PHE B 342 TRP 0.018 0.001 TRP B 415 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 8657) covalent geometry : angle 0.80247 / 0.40 (11784) hydrogen bonds : bond 0.04788 / 3.22 ( 615) hydrogen bonds : angle 5.03141 / 3.61 ( 1815) Misc. bond : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8933 (m-80) cc_final: 0.8240 (m-80) REVERT: A 26 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8150 (mmmt) REVERT: A 35 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (m110) REVERT: A 180 ARG cc_start: 0.6888 (ttt-90) cc_final: 0.6632 (mmm160) REVERT: A 187 GLN cc_start: 0.8848 (mt0) cc_final: 0.8613 (mt0) REVERT: A 214 MET cc_start: 0.9059 (mmm) cc_final: 0.8857 (mmm) REVERT: A 263 MET cc_start: 0.8765 (mtm) cc_final: 0.7557 (mtp) REVERT: A 292 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7108 (ptp90) REVERT: A 339 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7377 (p0) REVERT: A 351 LEU cc_start: 0.9107 (tp) cc_final: 0.8639 (tt) REVERT: A 418 GLN cc_start: 0.8054 (mp10) cc_final: 0.7625 (mp10) REVERT: A 444 THR cc_start: 0.9005 (m) cc_final: 0.8724 (p) REVERT: B 82 GLU cc_start: 0.8487 (pm20) cc_final: 0.8013 (pm20) REVERT: B 83 MET cc_start: 0.7752 (tpt) cc_final: 0.7482 (tpt) REVERT: B 90 LEU cc_start: 0.9097 (mt) cc_final: 0.8854 (mt) REVERT: B 120 ILE cc_start: 0.8515 (mt) cc_final: 0.8118 (mm) REVERT: B 122 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 124 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 156 MET cc_start: 0.7501 (tpp) cc_final: 0.6264 (tmm) REVERT: B 194 MET cc_start: 0.5257 (mtm) cc_final: 0.4961 (mtm) REVERT: B 290 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5929 (tm-30) REVERT: B 321 GLN cc_start: 0.7926 (tt0) cc_final: 0.7358 (pp30) REVERT: B 331 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8211 (tt0) REVERT: B 333 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (mp) REVERT: B 341 ARG cc_start: 0.5843 (mtm-85) cc_final: 0.5178 (ttp80) REVERT: B 379 PHE cc_start: 0.8282 (m-80) cc_final: 0.7601 (m-10) REVERT: B 395 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8349 (t0) REVERT: B 399 GLN cc_start: 0.7856 (mt0) cc_final: 0.7647 (mt0) REVERT: B 411 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7951 (m) REVERT: B 450 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5897 (p0) REVERT: C 406 MET cc_start: 0.7893 (pp-130) cc_final: 0.6991 (mtp) REVERT: C 412 LEU cc_start: 0.8748 (mm) cc_final: 0.8274 (tp) REVERT: C 423 GLU cc_start: 0.8769 (mp0) cc_final: 0.8320 (mp0) REVERT: C 471 GLN cc_start: 0.8183 (mt0) cc_final: 0.7829 (mt0) REVERT: C 474 GLN cc_start: 0.8068 (mt0) cc_final: 0.7601 (mt0) REVERT: D 483 PHE cc_start: 0.8637 (t80) cc_final: 0.8310 (t80) REVERT: D 501 GLN cc_start: 0.8513 (tt0) cc_final: 0.8145 (tt0) outliers start: 63 outliers final: 33 residues processed: 365 average time/residue: 0.0706 time to fit residues: 37.7306 Evaluate side-chains 339 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [96, 21, 45, 19, 71, 103, 95, 37, 107, 102, 49] chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 222 ASN A 339 ASN B 187 GLN C 458 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097385 restraints weight = 20394.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100192 restraints weight = 10762.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102067 restraints weight = 6924.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103235 restraints weight = 5124.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104031 restraints weight = 4216.694| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8658 Z= 0.169 Angle : 0.827 13.112 11784 Z= 0.412 Chirality : 0.048 0.326 1417 Planarity : 0.005 0.078 1458 Dihedral : 10.315 166.949 1220 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.04 % Favored : 93.24 % Rotamer: Outliers : 6.15 % Allowed : 32.80 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.79 (0.26), residues: 1109 helix: 1.70 (0.18), residues: 772 sheet: -1.87 (0.66), residues: 61 loop : -2.38 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 425 TYR 0.016 0.002 TYR B 106 PHE 0.049 0.002 PHE B 126 TRP 0.013 0.001 TRP B 415 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8657) covalent geometry : angle 0.82743 / 0.41 (11784) hydrogen bonds : bond 0.04744 / 3.19 ( 615) hydrogen bonds : angle 5.05701 / 3.62 ( 1815) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8915 (m-80) cc_final: 0.8220 (m-80) REVERT: A 26 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8131 (mmmt) REVERT: A 180 ARG cc_start: 0.6997 (ttt-90) cc_final: 0.6746 (mmm160) REVERT: A 292 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7103 (ptp90) REVERT: A 339 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 351 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 361 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: A 418 GLN cc_start: 0.8158 (mp10) cc_final: 0.7697 (mp10) REVERT: A 444 THR cc_start: 0.9096 (m) cc_final: 0.8766 (p) REVERT: B 35 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7614 (t0) REVERT: B 82 GLU cc_start: 0.8516 (pm20) cc_final: 0.8023 (pm20) REVERT: B 90 LEU cc_start: 0.9114 (mt) cc_final: 0.8886 (mt) REVERT: B 120 ILE cc_start: 0.8528 (mt) cc_final: 0.8156 (mm) REVERT: B 122 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 124 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 156 MET cc_start: 0.7552 (tpp) cc_final: 0.5991 (tmm) REVERT: B 187 GLN cc_start: 0.8392 (mt0) cc_final: 0.8171 (mt0) REVERT: B 263 MET cc_start: 0.9066 (tpp) cc_final: 0.8847 (ttt) REVERT: B 294 ILE cc_start: 0.7669 (tp) cc_final: 0.7463 (tp) REVERT: B 317 MET cc_start: 0.8828 (tmm) cc_final: 0.8317 (tpt) REVERT: B 321 GLN cc_start: 0.7855 (tt0) cc_final: 0.7333 (pp30) REVERT: B 331 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8289 (tt0) REVERT: B 333 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 341 ARG cc_start: 0.5955 (mtm-85) cc_final: 0.5485 (ttp80) REVERT: B 379 PHE cc_start: 0.8380 (m-80) cc_final: 0.7569 (m-10) REVERT: B 395 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 411 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7958 (m) REVERT: B 446 MET cc_start: 0.7960 (ttm) cc_final: 0.7581 (ttm) REVERT: C 406 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6947 (mtp) REVERT: C 412 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 423 GLU cc_start: 0.8753 (mp0) cc_final: 0.8326 (mp0) REVERT: C 474 GLN cc_start: 0.8109 (mt0) cc_final: 0.7549 (mt0) REVERT: C 506 MET cc_start: 0.7890 (mtt) cc_final: 0.5954 (mtt) REVERT: D 480 PHE cc_start: 0.8601 (t80) cc_final: 0.8302 (t80) REVERT: D 483 PHE cc_start: 0.8605 (t80) cc_final: 0.8225 (t80) REVERT: D 501 GLN cc_start: 0.8551 (tt0) cc_final: 0.8166 (tt0) REVERT: D 502 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8890 (ttm-80) outliers start: 54 outliers final: 33 residues processed: 339 average time/residue: 0.0704 time to fit residues: 34.9566 Evaluate side-chains 330 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [38, 42, 89, 82, 65, 63, 19, 60, 35, 67, 27] chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098616 restraints weight = 20566.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101499 restraints weight = 10817.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103373 restraints weight = 6950.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104582 restraints weight = 5163.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105334 restraints weight = 4251.888| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.8312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8658 Z= 0.163 Angle : 0.829 13.310 11784 Z= 0.415 Chirality : 0.048 0.329 1417 Planarity : 0.005 0.055 1458 Dihedral : 10.056 167.555 1215 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.40 % Favored : 92.88 % Rotamer: Outliers : 6.61 % Allowed : 32.57 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.87 (0.26), residues: 1109 helix: 1.70 (0.18), residues: 774 sheet: -1.67 (0.66), residues: 61 loop : -2.22 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 350 TYR 0.019 0.002 TYR B 106 PHE 0.053 0.002 PHE B 126 TRP 0.034 0.001 TRP A 415 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 8657) covalent geometry : angle 0.82883 / 0.41 (11784) hydrogen bonds : bond 0.04669 / 3.14 ( 615) hydrogen bonds : angle 5.01848 / 3.62 ( 1815) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 307 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8894 (m-80) cc_final: 0.8210 (m-80) REVERT: A 26 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8170 (mmmt) REVERT: A 180 ARG cc_start: 0.6990 (ttt-90) cc_final: 0.6639 (mmm160) REVERT: A 214 MET cc_start: 0.8735 (mmm) cc_final: 0.8444 (mmm) REVERT: A 292 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7043 (ptp90) REVERT: A 321 GLN cc_start: 0.8947 (pm20) cc_final: 0.8543 (mp10) REVERT: A 339 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7691 (p0) REVERT: A 351 LEU cc_start: 0.8987 (tp) cc_final: 0.8508 (tt) REVERT: A 418 GLN cc_start: 0.8162 (mp10) cc_final: 0.7671 (mp10) REVERT: A 444 THR cc_start: 0.9149 (m) cc_final: 0.8849 (p) REVERT: B 26 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7901 (mmmt) REVERT: B 35 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 82 GLU cc_start: 0.8457 (pm20) cc_final: 0.8023 (pm20) REVERT: B 90 LEU cc_start: 0.9108 (mt) cc_final: 0.8897 (mt) REVERT: B 120 ILE cc_start: 0.8515 (mt) cc_final: 0.8194 (mm) REVERT: B 124 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 154 PRO cc_start: 0.7043 (Cg_exo) cc_final: 0.6765 (Cg_endo) REVERT: B 156 MET cc_start: 0.7539 (tpp) cc_final: 0.6050 (tmm) REVERT: B 194 MET cc_start: 0.5638 (mtm) cc_final: 0.5249 (mtm) REVERT: B 290 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5961 (tm-30) REVERT: B 291 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6360 (m-70) REVERT: B 317 MET cc_start: 0.8776 (tmm) cc_final: 0.8101 (tpt) REVERT: B 321 GLN cc_start: 0.7782 (tt0) cc_final: 0.7279 (pp30) REVERT: B 331 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8333 (tt0) REVERT: B 333 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 379 PHE cc_start: 0.8362 (m-80) cc_final: 0.7566 (m-10) REVERT: B 395 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8188 (t0) REVERT: C 406 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7037 (mtp) REVERT: C 412 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8312 (tp) REVERT: C 423 GLU cc_start: 0.8770 (mp0) cc_final: 0.8350 (mp0) REVERT: C 474 GLN cc_start: 0.8114 (mt0) cc_final: 0.7808 (mt0) REVERT: C 503 MET cc_start: 0.9415 (mtp) cc_final: 0.8673 (mtp) REVERT: D 480 PHE cc_start: 0.8511 (t80) cc_final: 0.8261 (t80) REVERT: D 483 PHE cc_start: 0.8536 (t80) cc_final: 0.8074 (t80) REVERT: D 501 GLN cc_start: 0.8611 (tt0) cc_final: 0.8237 (tt0) REVERT: D 502 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8726 (ttm170) outliers start: 58 outliers final: 36 residues processed: 338 average time/residue: 0.0667 time to fit residues: 32.6685 Evaluate side-chains 330 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [75, 107, 87, 17, 30, 39, 73, 21, 51, 94, 80] chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 187 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.122904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099417 restraints weight = 20342.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102246 restraints weight = 10804.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104094 restraints weight = 6962.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105340 restraints weight = 5174.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106038 restraints weight = 4254.880| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8658 Z= 0.166 Angle : 0.852 13.498 11784 Z= 0.424 Chirality : 0.049 0.337 1417 Planarity : 0.005 0.055 1458 Dihedral : 10.013 167.182 1215 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.40 % Favored : 92.88 % Rotamer: Outliers : 5.24 % Allowed : 35.08 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.82 (0.26), residues: 1109 helix: 1.61 (0.18), residues: 777 sheet: -1.39 (0.68), residues: 62 loop : -2.19 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 265 TYR 0.020 0.002 TYR D 439 PHE 0.055 0.002 PHE B 126 TRP 0.023 0.001 TRP A 415 HIS 0.004 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 8657) covalent geometry : angle 0.85215 / 0.42 (11784) hydrogen bonds : bond 0.04726 / 3.19 ( 615) hydrogen bonds : angle 5.07646 / 3.68 ( 1815) Misc. bond : bond 0.00094 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8894 (m-80) cc_final: 0.8207 (m-80) REVERT: A 26 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8174 (mmmt) REVERT: A 180 ARG cc_start: 0.7020 (ttt-90) cc_final: 0.6685 (mmm160) REVERT: A 214 MET cc_start: 0.8832 (mmm) cc_final: 0.8533 (mmm) REVERT: A 291 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.6073 (m-70) REVERT: A 292 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6909 (ptp90) REVERT: A 321 GLN cc_start: 0.8994 (pm20) cc_final: 0.8562 (mp10) REVERT: A 351 LEU cc_start: 0.8882 (tp) cc_final: 0.8586 (tt) REVERT: A 418 GLN cc_start: 0.8157 (mp10) cc_final: 0.7720 (mp10) REVERT: A 439 PHE cc_start: 0.8516 (m-10) cc_final: 0.8222 (m-80) REVERT: A 444 THR cc_start: 0.9185 (m) cc_final: 0.8791 (p) REVERT: B 26 LYS cc_start: 0.8220 (mmmt) cc_final: 0.8000 (mmmt) REVERT: B 82 GLU cc_start: 0.8464 (pm20) cc_final: 0.8014 (pm20) REVERT: B 90 LEU cc_start: 0.9101 (mt) cc_final: 0.8873 (mt) REVERT: B 120 ILE cc_start: 0.8665 (mt) cc_final: 0.8283 (mm) REVERT: B 124 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 156 MET cc_start: 0.7566 (tpp) cc_final: 0.6132 (tmm) REVERT: B 187 GLN cc_start: 0.8301 (mt0) cc_final: 0.8020 (mt0) REVERT: B 291 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6621 (m-70) REVERT: B 317 MET cc_start: 0.8701 (tmm) cc_final: 0.7503 (tpt) REVERT: B 321 GLN cc_start: 0.7755 (tt0) cc_final: 0.7262 (pp30) REVERT: B 331 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8354 (tt0) REVERT: B 336 ARG cc_start: 0.8722 (ttt-90) cc_final: 0.8469 (ttt180) REVERT: B 341 ARG cc_start: 0.5989 (ptm160) cc_final: 0.5585 (ptm160) REVERT: B 370 LEU cc_start: 0.7279 (mt) cc_final: 0.7017 (mt) REVERT: B 379 PHE cc_start: 0.8354 (m-80) cc_final: 0.7719 (m-10) REVERT: B 395 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8170 (t0) REVERT: B 446 MET cc_start: 0.7710 (ttm) cc_final: 0.7303 (ttm) REVERT: C 406 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6991 (mtp) REVERT: C 412 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8308 (tp) REVERT: C 423 GLU cc_start: 0.8756 (mp0) cc_final: 0.8342 (mp0) REVERT: C 474 GLN cc_start: 0.8105 (mt0) cc_final: 0.7757 (mt0) REVERT: D 480 PHE cc_start: 0.8523 (t80) cc_final: 0.8151 (t80) REVERT: D 483 PHE cc_start: 0.8452 (t80) cc_final: 0.7980 (t80) REVERT: D 501 GLN cc_start: 0.8595 (tt0) cc_final: 0.8221 (tt0) outliers start: 46 outliers final: 32 residues processed: 335 average time/residue: 0.0729 time to fit residues: 35.4588 Evaluate side-chains 325 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [98, 79, 38, 57, 1, 91, 78, 0, 89, 33, 95] chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099264 restraints weight = 20187.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102103 restraints weight = 10782.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104014 restraints weight = 6971.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105285 restraints weight = 5179.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105998 restraints weight = 4242.124| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8658 Z= 0.166 Angle : 0.878 15.044 11784 Z= 0.432 Chirality : 0.049 0.313 1417 Planarity : 0.005 0.056 1458 Dihedral : 9.945 168.417 1212 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.85 % Favored : 92.52 % Rotamer: Outliers : 4.78 % Allowed : 36.67 % Favored : 58.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.84 (0.26), residues: 1109 helix: 1.58 (0.18), residues: 772 sheet: -0.79 (0.74), residues: 55 loop : -2.09 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 350 TYR 0.022 0.002 TYR B 106 PHE 0.053 0.002 PHE B 126 TRP 0.019 0.001 TRP A 415 HIS 0.005 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 8657) covalent geometry : angle 0.87766 / 0.43 (11784) hydrogen bonds : bond 0.04740 / 3.20 ( 615) hydrogen bonds : angle 5.11917 / 3.69 ( 1815) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8905 (m-80) cc_final: 0.8214 (m-80) REVERT: A 26 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8161 (mmmt) REVERT: A 180 ARG cc_start: 0.6987 (ttt-90) cc_final: 0.6684 (mmm160) REVERT: A 214 MET cc_start: 0.8876 (mmm) cc_final: 0.8567 (mmm) REVERT: A 235 MET cc_start: 0.8009 (ptp) cc_final: 0.7789 (ptp) REVERT: A 291 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.6033 (m-70) REVERT: A 351 LEU cc_start: 0.8765 (tp) cc_final: 0.8434 (tt) REVERT: A 418 GLN cc_start: 0.8169 (mp10) cc_final: 0.7699 (mp10) REVERT: A 439 PHE cc_start: 0.8560 (m-10) cc_final: 0.8255 (m-80) REVERT: A 444 THR cc_start: 0.9190 (m) cc_final: 0.8797 (p) REVERT: B 26 LYS cc_start: 0.8293 (mmmt) cc_final: 0.8079 (mmmt) REVERT: B 82 GLU cc_start: 0.8493 (pm20) cc_final: 0.8008 (pm20) REVERT: B 90 LEU cc_start: 0.9100 (mt) cc_final: 0.8875 (mt) REVERT: B 120 ILE cc_start: 0.8700 (mt) cc_final: 0.8343 (tp) REVERT: B 124 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 156 MET cc_start: 0.7642 (tpp) cc_final: 0.6184 (tmm) REVERT: B 187 GLN cc_start: 0.8320 (mt0) cc_final: 0.8002 (mt0) REVERT: B 291 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6548 (m-70) REVERT: B 321 GLN cc_start: 0.7743 (tt0) cc_final: 0.7340 (pp30) REVERT: B 331 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8234 (tt0) REVERT: B 336 ARG cc_start: 0.8710 (ttt-90) cc_final: 0.8458 (ttt180) REVERT: B 341 ARG cc_start: 0.6091 (ptm160) cc_final: 0.5259 (ttp80) REVERT: B 379 PHE cc_start: 0.8364 (m-80) cc_final: 0.7634 (m-10) REVERT: B 395 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8127 (t0) REVERT: B 446 MET cc_start: 0.7667 (ttm) cc_final: 0.7171 (ttm) REVERT: C 406 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6915 (mtp) REVERT: C 412 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 423 GLU cc_start: 0.8754 (mp0) cc_final: 0.8348 (mp0) REVERT: C 474 GLN cc_start: 0.8090 (mt0) cc_final: 0.7746 (mt0) REVERT: D 405 LEU cc_start: 0.7776 (mt) cc_final: 0.7561 (tp) REVERT: D 480 PHE cc_start: 0.8518 (t80) cc_final: 0.8140 (t80) REVERT: D 483 PHE cc_start: 0.8469 (t80) cc_final: 0.8084 (t80) REVERT: D 501 GLN cc_start: 0.8621 (tt0) cc_final: 0.8265 (tt0) outliers start: 42 outliers final: 32 residues processed: 321 average time/residue: 0.0693 time to fit residues: 32.4930 Evaluate side-chains 324 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [14, 70, 105, 104, 89, 53, 80, 72, 107, 47, 31] chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099862 restraints weight = 20177.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102768 restraints weight = 10908.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104675 restraints weight = 7067.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105895 restraints weight = 5249.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.106439 restraints weight = 4315.002| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.8899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8658 Z= 0.169 Angle : 0.915 15.597 11784 Z= 0.450 Chirality : 0.051 0.351 1417 Planarity : 0.005 0.057 1458 Dihedral : 9.677 169.554 1206 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.49 % Favored : 92.88 % Rotamer: Outliers : 3.99 % Allowed : 38.27 % Favored : 57.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.80 (0.26), residues: 1109 helix: 1.50 (0.19), residues: 777 sheet: -1.10 (0.69), residues: 62 loop : -1.97 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 350 TYR 0.033 0.002 TYR A 106 PHE 0.053 0.002 PHE B 126 TRP 0.018 0.001 TRP A 415 HIS 0.004 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8657) covalent geometry : angle 0.91544 / 0.45 (11784) hydrogen bonds : bond 0.04725 / 3.21 ( 615) hydrogen bonds : angle 5.15784 / 3.75 ( 1815) Misc. bond : bond 0.00093 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8885 (m-80) cc_final: 0.8177 (m-80) REVERT: A 180 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6721 (mmm160) REVERT: A 214 MET cc_start: 0.8832 (mmm) cc_final: 0.8521 (mmm) REVERT: A 321 GLN cc_start: 0.9014 (pm20) cc_final: 0.8620 (pm20) REVERT: A 351 LEU cc_start: 0.8867 (tp) cc_final: 0.8592 (tt) REVERT: A 409 MET cc_start: 0.8026 (mmm) cc_final: 0.7091 (mmm) REVERT: A 418 GLN cc_start: 0.8202 (mp10) cc_final: 0.7839 (mp10) REVERT: A 444 THR cc_start: 0.9268 (m) cc_final: 0.8995 (p) REVERT: B 82 GLU cc_start: 0.8459 (pm20) cc_final: 0.8146 (pm20) REVERT: B 120 ILE cc_start: 0.8619 (mt) cc_final: 0.8245 (tp) REVERT: B 124 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 156 MET cc_start: 0.7662 (tpp) cc_final: 0.6234 (tmm) REVERT: B 291 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.5852 (m-70) REVERT: B 317 MET cc_start: 0.8645 (tmm) cc_final: 0.7888 (tpt) REVERT: B 321 GLN cc_start: 0.7792 (tt0) cc_final: 0.7356 (pp30) REVERT: B 331 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8249 (tt0) REVERT: B 336 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8472 (ttt180) REVERT: B 341 ARG cc_start: 0.6213 (ptm160) cc_final: 0.5286 (ttp80) REVERT: B 379 PHE cc_start: 0.8369 (m-80) cc_final: 0.7594 (m-10) REVERT: B 395 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8065 (t0) REVERT: B 446 MET cc_start: 0.7600 (ttm) cc_final: 0.7301 (ptp) REVERT: C 406 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7301 (ptm) REVERT: C 412 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8284 (tp) REVERT: C 423 GLU cc_start: 0.8721 (mp0) cc_final: 0.8326 (mp0) REVERT: C 474 GLN cc_start: 0.8103 (mt0) cc_final: 0.7892 (mt0) REVERT: D 480 PHE cc_start: 0.8483 (t80) cc_final: 0.8114 (t80) REVERT: D 483 PHE cc_start: 0.8471 (t80) cc_final: 0.8145 (t80) REVERT: D 501 GLN cc_start: 0.8615 (tt0) cc_final: 0.8276 (tt0) outliers start: 35 outliers final: 27 residues processed: 311 average time/residue: 0.0739 time to fit residues: 33.8100 Evaluate side-chains 318 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [34, 38, 90, 81, 29, 14, 17, 74, 91, 18, 67] chunk 34 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101448 restraints weight = 19964.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.104357 restraints weight = 10801.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106262 restraints weight = 7013.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107552 restraints weight = 5210.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108117 restraints weight = 4268.452| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.9138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8658 Z= 0.165 Angle : 0.918 16.261 11784 Z= 0.451 Chirality : 0.051 0.369 1417 Planarity : 0.005 0.059 1458 Dihedral : 9.573 170.138 1204 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.49 % Favored : 92.88 % Rotamer: Outliers : 3.76 % Allowed : 38.50 % Favored : 57.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.82 (0.26), residues: 1109 helix: 1.52 (0.18), residues: 775 sheet: -0.67 (0.71), residues: 55 loop : -2.02 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 350 TYR 0.022 0.002 TYR D 439 PHE 0.053 0.002 PHE B 126 TRP 0.013 0.001 TRP A 415 HIS 0.010 0.001 HIS B 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8657) covalent geometry : angle 0.91821 / 0.45 (11784) hydrogen bonds : bond 0.04653 / 3.16 ( 615) hydrogen bonds : angle 5.09341 / 3.71 ( 1815) Misc. bond : bond 0.00087 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.77 seconds wall clock time: 27 minutes 5.00 seconds (1625.00 seconds total)