Starting phenix.real_space_refine on Fri Jun 6 00:42:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivw_60935/06_2025/9ivw_60935.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4366 2.51 5 N 1205 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6852 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3074 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "F" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3778 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 27, 'TRANS': 441} Chain breaks: 4 Time building chain proxies: 4.64, per 1000 atoms: 0.68 Number of scatterers: 6852 At special positions: 0 Unit cell: (107.5, 93.75, 138.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1235 8.00 N 1205 7.00 C 4366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 515 " - pdb=" SG CYS F 516 " distance=2.03 Simple disulfide: pdb=" SG CYS G 516 " - pdb=" SG CYS F 515 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 997.9 milliseconds 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 3 sheets defined 60.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'G' and resid 189 through 195 removed outlier: 3.652A pdb=" N GLN G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.212A pdb=" N GLY G 305 " --> pdb=" O GLN G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 319 Processing helix chain 'G' and resid 322 through 352 removed outlier: 5.263A pdb=" N VAL G 341 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP G 352 " --> pdb=" O ARG G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 368 Processing helix chain 'G' and resid 370 through 380 Processing helix chain 'G' and resid 382 through 386 removed outlier: 4.244A pdb=" N ASN G 385 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 407 removed outlier: 3.630A pdb=" N SER G 405 " --> pdb=" O VAL G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 438 Processing helix chain 'G' and resid 440 through 460 removed outlier: 5.479A pdb=" N LYS G 456 " --> pdb=" O LYS G 452 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP G 457 " --> pdb=" O GLN G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 476 Processing helix chain 'G' and resid 477 through 486 Processing helix chain 'G' and resid 493 through 509 Processing helix chain 'G' and resid 518 through 523 removed outlier: 3.659A pdb=" N ASP G 521 " --> pdb=" O LEU G 518 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 523 " --> pdb=" O SER G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 533 No H-bonds generated for 'chain 'G' and resid 531 through 533' Processing helix chain 'G' and resid 534 through 551 Processing helix chain 'F' and resid 183 through 188 removed outlier: 4.987A pdb=" N SER F 188 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 195 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.941A pdb=" N LEU F 256 " --> pdb=" O ARG F 252 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.552A pdb=" N VAL F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.905A pdb=" N LEU F 326 " --> pdb=" O GLU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 352 through 368 Processing helix chain 'F' and resid 370 through 380 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 408 through 438 removed outlier: 3.746A pdb=" N ARG F 413 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 459 removed outlier: 3.546A pdb=" N LYS F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS F 456 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP F 457 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 Processing helix chain 'F' and resid 477 through 486 Processing helix chain 'F' and resid 493 through 508 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 526 through 530 Processing helix chain 'F' and resid 531 through 533 No H-bonds generated for 'chain 'F' and resid 531 through 533' Processing helix chain 'F' and resid 534 through 551 Processing helix chain 'F' and resid 581 through 590 removed outlier: 3.650A pdb=" N ILE F 590 " --> pdb=" O SER F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 removed outlier: 3.566A pdb=" N TRP F 617 " --> pdb=" O THR F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 678 removed outlier: 3.761A pdb=" N LEU F 660 " --> pdb=" O GLN F 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 176 through 177 removed outlier: 3.554A pdb=" N CYS G 177 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 174 through 176 Processing sheet with id=AA3, first strand: chain 'F' and resid 386 through 387 342 hydrogen bonds defined for protein. 984 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: 1.77 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1134 1.28 - 1.41: 1711 1.41 - 1.55: 4085 1.55 - 1.69: 2 1.69 - 1.82: 64 Bond restraints: 6996 Sorted by residual: bond pdb=" C ASP G 521 " pdb=" N PHE G 522 " ideal model delta sigma weight residual 1.328 1.446 -0.119 1.13e-02 7.83e+03 1.10e+02 bond pdb=" C HIS F 470 " pdb=" O HIS F 470 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.22e-02 6.72e+03 6.28e+01 bond pdb=" C VAL F 416 " pdb=" O VAL F 416 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.12e-02 7.97e+03 4.54e+01 bond pdb=" C VAL F 255 " pdb=" O VAL F 255 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.19e-02 7.06e+03 3.19e+01 bond pdb=" C ASP G 418 " pdb=" O ASP G 418 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.19e-02 7.06e+03 2.97e+01 ... (remaining 6991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 8885 2.11 - 4.21: 482 4.21 - 6.32: 89 6.32 - 8.43: 17 8.43 - 10.53: 3 Bond angle restraints: 9476 Sorted by residual: angle pdb=" N CYS G 345 " pdb=" CA CYS G 345 " pdb=" C CYS G 345 " ideal model delta sigma weight residual 111.28 103.84 7.44 1.09e+00 8.42e-01 4.65e+01 angle pdb=" CA VAL G 262 " pdb=" C VAL G 262 " pdb=" O VAL G 262 " ideal model delta sigma weight residual 121.97 115.77 6.20 9.80e-01 1.04e+00 4.00e+01 angle pdb=" N GLU G 506 " pdb=" CA GLU G 506 " pdb=" C GLU G 506 " ideal model delta sigma weight residual 110.97 104.09 6.88 1.09e+00 8.42e-01 3.98e+01 angle pdb=" N GLN G 347 " pdb=" CA GLN G 347 " pdb=" C GLN G 347 " ideal model delta sigma weight residual 111.02 103.35 7.67 1.22e+00 6.72e-01 3.95e+01 angle pdb=" CB GLU F 464 " pdb=" CG GLU F 464 " pdb=" CD GLU F 464 " ideal model delta sigma weight residual 112.60 123.13 -10.53 1.70e+00 3.46e-01 3.84e+01 ... (remaining 9471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3573 17.95 - 35.90: 493 35.90 - 53.86: 174 53.86 - 71.81: 32 71.81 - 89.76: 18 Dihedral angle restraints: 4290 sinusoidal: 1790 harmonic: 2500 Sorted by residual: dihedral pdb=" CB CYS G 515 " pdb=" SG CYS G 515 " pdb=" SG CYS F 516 " pdb=" CB CYS F 516 " ideal model delta sinusoidal sigma weight residual -86.00 -137.14 51.14 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS G 516 " pdb=" SG CYS G 516 " pdb=" SG CYS F 515 " pdb=" CB CYS F 515 " ideal model delta sinusoidal sigma weight residual -86.00 -123.98 37.98 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" C ASP G 457 " pdb=" N ASP G 457 " pdb=" CA ASP G 457 " pdb=" CB ASP G 457 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 4287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 864 0.058 - 0.117: 146 0.117 - 0.175: 36 0.175 - 0.234: 8 0.234 - 0.292: 5 Chirality restraints: 1059 Sorted by residual: chirality pdb=" CA ASP G 457 " pdb=" N ASP G 457 " pdb=" C ASP G 457 " pdb=" CB ASP G 457 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA SER G 508 " pdb=" N SER G 508 " pdb=" C SER G 508 " pdb=" CB SER G 508 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA LEU F 181 " pdb=" N LEU F 181 " pdb=" C LEU F 181 " pdb=" CB LEU F 181 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1056 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 259 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C SER F 259 " -0.083 2.00e-02 2.50e+03 pdb=" O SER F 259 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE F 260 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 281 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C MET F 281 " -0.078 2.00e-02 2.50e+03 pdb=" O MET F 281 " 0.029 2.00e-02 2.50e+03 pdb=" N SER F 282 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 463 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C ASN F 463 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN F 463 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU F 464 " 0.019 2.00e-02 2.50e+03 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1630 2.79 - 3.32: 7314 3.32 - 3.85: 11138 3.85 - 4.37: 12295 4.37 - 4.90: 20267 Nonbonded interactions: 52644 Sorted by model distance: nonbonded pdb=" O LEU F 585 " pdb=" OG SER F 588 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASP F 311 " pdb=" NH2 ARG F 330 " model vdw 2.285 3.120 nonbonded pdb=" N LEU F 246 " pdb=" OD2 ASP F 249 " model vdw 2.308 3.120 nonbonded pdb=" O SER F 508 " pdb=" OG SER F 508 " model vdw 2.346 3.040 nonbonded pdb=" N GLY F 199 " pdb=" O ILE F 635 " model vdw 2.346 3.120 ... (remaining 52639 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.820 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.007 0.119 6998 Z= 0.484 Angle : 1.060 10.532 9480 Z= 0.721 Chirality : 0.054 0.292 1059 Planarity : 0.006 0.054 1227 Dihedral : 19.238 89.759 2654 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.74 % Allowed : 28.70 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.30), residues: 835 helix: 0.63 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 459 HIS 0.005 0.001 HIS F 658 PHE 0.021 0.001 PHE G 503 TYR 0.016 0.001 TYR G 546 ARG 0.008 0.001 ARG F 417 Details of bonding type rmsd hydrogen bonds : bond 0.17027 ( 342) hydrogen bonds : angle 6.41121 ( 984) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.73391 ( 4) covalent geometry : bond 0.00663 ( 6996) covalent geometry : angle 1.05992 ( 9476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 410 time to evaluate : 0.792 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: symmetry clash REVERT: G 171 HIS cc_start: 0.7700 (m-70) cc_final: 0.7221 (m-70) REVERT: G 181 LEU cc_start: 0.8640 (mp) cc_final: 0.8039 (pt) REVERT: G 184 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7544 (ttp80) REVERT: G 223 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7971 (mtmm) REVERT: G 247 GLU cc_start: 0.7712 (mp0) cc_final: 0.7239 (mp0) REVERT: G 252 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7975 (ttt-90) REVERT: G 285 ILE cc_start: 0.8474 (mm) cc_final: 0.8215 (mm) REVERT: G 288 ARG cc_start: 0.7439 (tpp-160) cc_final: 0.6864 (mmm160) REVERT: G 290 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7605 (mtp85) REVERT: G 299 GLN cc_start: 0.8617 (mp10) cc_final: 0.8250 (mp10) REVERT: G 327 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7842 (tm-30) REVERT: G 333 MET cc_start: 0.8510 (ptm) cc_final: 0.8162 (ptp) REVERT: G 344 GLU cc_start: 0.8344 (tp30) cc_final: 0.7051 (tp30) REVERT: G 347 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (tm-30) REVERT: G 348 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8487 (mtm-85) REVERT: G 355 MET cc_start: 0.7289 (tpp) cc_final: 0.6701 (tpp) REVERT: G 359 LEU cc_start: 0.8853 (mt) cc_final: 0.8353 (mm) REVERT: G 412 ARG cc_start: 0.8464 (ttt180) cc_final: 0.7894 (ptm-80) REVERT: G 419 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8533 (m) REVERT: G 420 VAL cc_start: 0.9276 (p) cc_final: 0.9029 (p) REVERT: G 421 TYR cc_start: 0.7995 (t80) cc_final: 0.7612 (t80) REVERT: G 422 LEU cc_start: 0.8626 (mt) cc_final: 0.8387 (mt) REVERT: G 423 PHE cc_start: 0.8558 (t80) cc_final: 0.8315 (t80) REVERT: G 424 LEU cc_start: 0.9057 (mt) cc_final: 0.8767 (mt) REVERT: G 425 CYS cc_start: 0.8978 (m) cc_final: 0.8511 (m) REVERT: G 426 TYR cc_start: 0.8598 (t80) cc_final: 0.8016 (t80) REVERT: G 428 TRP cc_start: 0.8623 (t-100) cc_final: 0.8310 (t-100) REVERT: G 429 GLN cc_start: 0.8267 (tt0) cc_final: 0.7755 (tt0) REVERT: G 443 ASN cc_start: 0.8806 (m110) cc_final: 0.8251 (m110) REVERT: G 444 LEU cc_start: 0.8824 (mm) cc_final: 0.8564 (mm) REVERT: G 445 LYS cc_start: 0.8809 (mptp) cc_final: 0.8397 (mptp) REVERT: G 446 GLU cc_start: 0.7506 (tt0) cc_final: 0.7225 (tt0) REVERT: G 447 LEU cc_start: 0.8727 (mp) cc_final: 0.8422 (mp) REVERT: G 448 GLN cc_start: 0.8250 (mt0) cc_final: 0.7350 (mt0) REVERT: G 451 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8360 (mt) REVERT: G 452 LYS cc_start: 0.8402 (mttm) cc_final: 0.7796 (mttm) REVERT: G 470 HIS cc_start: 0.8448 (m-70) cc_final: 0.8218 (m-70) REVERT: G 482 LYS cc_start: 0.8710 (tptp) cc_final: 0.8455 (tptp) REVERT: G 495 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8149 (p) REVERT: G 497 LEU cc_start: 0.9077 (mm) cc_final: 0.8823 (mm) REVERT: G 498 GLN cc_start: 0.8696 (tp40) cc_final: 0.8285 (tp40) REVERT: G 499 ASN cc_start: 0.8740 (m-40) cc_final: 0.8499 (m-40) REVERT: G 501 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8406 (ttp-170) REVERT: G 503 PHE cc_start: 0.8787 (t80) cc_final: 0.8493 (t80) REVERT: G 504 ILE cc_start: 0.8798 (mm) cc_final: 0.8543 (mm) REVERT: G 506 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7446 (mm-30) REVERT: G 507 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7587 (mmm-85) REVERT: G 518 LEU cc_start: 0.7990 (mt) cc_final: 0.7639 (pp) REVERT: F 167 LEU cc_start: 0.6373 (tp) cc_final: 0.5959 (mp) REVERT: F 170 TYR cc_start: 0.7156 (m-80) cc_final: 0.6451 (t80) REVERT: F 191 ASP cc_start: 0.8653 (p0) cc_final: 0.8167 (p0) REVERT: F 192 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8211 (mmtt) REVERT: F 194 LEU cc_start: 0.8614 (mt) cc_final: 0.8209 (mm) REVERT: F 196 LEU cc_start: 0.8391 (mt) cc_final: 0.8086 (mm) REVERT: F 198 GLN cc_start: 0.8026 (pm20) cc_final: 0.6883 (tp40) REVERT: F 215 PHE cc_start: 0.6607 (m-80) cc_final: 0.6170 (m-80) REVERT: F 313 GLN cc_start: 0.8466 (mm-40) cc_final: 0.7957 (pt0) REVERT: F 322 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7226 (pm20) REVERT: F 325 ASP cc_start: 0.7777 (m-30) cc_final: 0.6995 (m-30) REVERT: F 327 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8159 (mm-30) REVERT: F 333 MET cc_start: 0.7645 (tpp) cc_final: 0.7191 (mpp) REVERT: F 346 MET cc_start: 0.8082 (mtt) cc_final: 0.7430 (mtt) REVERT: F 347 GLN cc_start: 0.8478 (tp40) cc_final: 0.8056 (tp40) REVERT: F 348 ARG cc_start: 0.8452 (ptp-110) cc_final: 0.8159 (ptp-110) REVERT: F 349 PHE cc_start: 0.8465 (t80) cc_final: 0.8181 (t80) REVERT: F 355 MET cc_start: 0.8222 (tpp) cc_final: 0.7255 (tpp) REVERT: F 357 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8066 (ttt-90) REVERT: F 363 LEU cc_start: 0.9000 (mm) cc_final: 0.8599 (mt) REVERT: F 368 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.6791 (ttm-80) REVERT: F 371 TYR cc_start: 0.8269 (p90) cc_final: 0.7901 (p90) REVERT: F 374 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7749 (mm-40) REVERT: F 392 ILE cc_start: 0.7814 (tp) cc_final: 0.7490 (tp) REVERT: F 404 HIS cc_start: 0.8427 (p-80) cc_final: 0.8217 (p-80) REVERT: F 405 SER cc_start: 0.8763 (t) cc_final: 0.8551 (p) REVERT: F 415 TYR cc_start: 0.8805 (t80) cc_final: 0.8575 (t80) REVERT: F 429 GLN cc_start: 0.8654 (mt0) cc_final: 0.8344 (mt0) REVERT: F 434 VAL cc_start: 0.8207 (p) cc_final: 0.7546 (p) REVERT: F 446 GLU cc_start: 0.8382 (tt0) cc_final: 0.8094 (pt0) REVERT: F 448 GLN cc_start: 0.8816 (mt0) cc_final: 0.8281 (mt0) REVERT: F 480 LEU cc_start: 0.8258 (tt) cc_final: 0.7982 (tt) REVERT: F 495 SER cc_start: 0.8507 (t) cc_final: 0.8270 (p) REVERT: F 498 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7858 (tp40) REVERT: F 501 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7853 (ttp-110) REVERT: F 502 ASN cc_start: 0.7762 (t0) cc_final: 0.7157 (t0) REVERT: F 528 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.4433 (tmm-80) REVERT: F 538 CYS cc_start: 0.8372 (m) cc_final: 0.7888 (m) REVERT: F 539 TYR cc_start: 0.8133 (t80) cc_final: 0.7484 (t80) REVERT: F 573 THR cc_start: 0.7607 (p) cc_final: 0.7346 (t) REVERT: F 575 HIS cc_start: 0.8580 (m90) cc_final: 0.7983 (m90) REVERT: F 576 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7203 (mtm-85) REVERT: F 583 GLN cc_start: 0.8634 (mm110) cc_final: 0.8400 (mm110) REVERT: F 587 GLU cc_start: 0.8060 (tt0) cc_final: 0.7822 (tt0) REVERT: F 611 LYS cc_start: 0.8397 (pttt) cc_final: 0.8001 (mmtp) REVERT: F 614 PRO cc_start: 0.8511 (Cg_exo) cc_final: 0.8221 (Cg_endo) REVERT: F 617 TRP cc_start: 0.8161 (t60) cc_final: 0.7877 (t60) REVERT: F 621 TYR cc_start: 0.8504 (t80) cc_final: 0.8249 (t80) REVERT: F 628 GLU cc_start: 0.8226 (pt0) cc_final: 0.7851 (pt0) outliers start: 28 outliers final: 9 residues processed: 420 average time/residue: 0.2701 time to fit residues: 137.8997 Evaluate side-chains 386 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 370 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 419 CYS Chi-restraints excluded: chain G residue 432 MET Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain F residue 252 ARG Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 528 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 186 ASN F 347 GLN F 485 GLN F 537 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 664 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.102172 restraints weight = 14972.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106047 restraints weight = 7786.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108692 restraints weight = 4828.593| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6998 Z= 0.168 Angle : 0.773 11.324 9480 Z= 0.383 Chirality : 0.046 0.176 1059 Planarity : 0.005 0.044 1227 Dihedral : 7.954 65.217 976 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.74 % Allowed : 25.50 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.29), residues: 835 helix: 1.05 (0.24), residues: 462 sheet: -1.56 (1.57), residues: 12 loop : -1.17 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 317 HIS 0.004 0.001 HIS F 470 PHE 0.014 0.001 PHE F 423 TYR 0.016 0.002 TYR F 546 ARG 0.007 0.001 ARG F 417 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 342) hydrogen bonds : angle 4.76604 ( 984) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.86035 ( 4) covalent geometry : bond 0.00355 ( 6996) covalent geometry : angle 0.77287 ( 9476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 0.799 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: G 181 LEU cc_start: 0.8512 (mp) cc_final: 0.7884 (pt) REVERT: G 182 SER cc_start: 0.8481 (p) cc_final: 0.7757 (t) REVERT: G 184 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7673 (ttp80) REVERT: G 187 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.7573 (mpt180) REVERT: G 193 GLN cc_start: 0.8748 (mp10) cc_final: 0.8460 (mp10) REVERT: G 204 ASP cc_start: 0.7658 (t70) cc_final: 0.7317 (t0) REVERT: G 223 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7862 (mtmm) REVERT: G 288 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7041 (tpm170) REVERT: G 290 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7472 (mtp85) REVERT: G 299 GLN cc_start: 0.8560 (mp10) cc_final: 0.8283 (mp10) REVERT: G 312 GLU cc_start: 0.7936 (tm-30) cc_final: 0.6652 (tm-30) REVERT: G 316 ARG cc_start: 0.8767 (mtp180) cc_final: 0.8213 (mtp180) REVERT: G 327 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7958 (tm-30) REVERT: G 328 GLU cc_start: 0.8661 (pp20) cc_final: 0.8097 (pp20) REVERT: G 333 MET cc_start: 0.8424 (ptm) cc_final: 0.7819 (ptp) REVERT: G 344 GLU cc_start: 0.8135 (tp30) cc_final: 0.7028 (tp30) REVERT: G 348 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8510 (mmt90) REVERT: G 349 PHE cc_start: 0.8959 (t80) cc_final: 0.8604 (t80) REVERT: G 355 MET cc_start: 0.7550 (tpp) cc_final: 0.6798 (tpp) REVERT: G 359 LEU cc_start: 0.8997 (mt) cc_final: 0.8440 (mm) REVERT: G 408 LYS cc_start: 0.8297 (tppt) cc_final: 0.7268 (tppt) REVERT: G 412 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8018 (ttp-170) REVERT: G 417 ARG cc_start: 0.8726 (mtm110) cc_final: 0.8403 (mtm-85) REVERT: G 418 ASP cc_start: 0.8455 (t0) cc_final: 0.8206 (t70) REVERT: G 419 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8373 (m) REVERT: G 420 VAL cc_start: 0.9106 (p) cc_final: 0.8667 (p) REVERT: G 421 TYR cc_start: 0.8184 (t80) cc_final: 0.7666 (t80) REVERT: G 423 PHE cc_start: 0.8566 (t80) cc_final: 0.8339 (t80) REVERT: G 424 LEU cc_start: 0.8933 (mt) cc_final: 0.8691 (mt) REVERT: G 425 CYS cc_start: 0.8935 (m) cc_final: 0.8506 (m) REVERT: G 426 TYR cc_start: 0.8558 (t80) cc_final: 0.8151 (t80) REVERT: G 428 TRP cc_start: 0.8743 (t-100) cc_final: 0.8524 (t-100) REVERT: G 429 GLN cc_start: 0.8339 (tt0) cc_final: 0.7918 (tt0) REVERT: G 432 MET cc_start: 0.7927 (mmm) cc_final: 0.7372 (mmm) REVERT: G 443 ASN cc_start: 0.8595 (m110) cc_final: 0.8089 (m110) REVERT: G 444 LEU cc_start: 0.8801 (mm) cc_final: 0.8593 (mm) REVERT: G 445 LYS cc_start: 0.8783 (mptp) cc_final: 0.8364 (mptp) REVERT: G 446 GLU cc_start: 0.7557 (tt0) cc_final: 0.7028 (pt0) REVERT: G 448 GLN cc_start: 0.8363 (mt0) cc_final: 0.7278 (mt0) REVERT: G 452 LYS cc_start: 0.8528 (mttm) cc_final: 0.7896 (mttm) REVERT: G 453 GLN cc_start: 0.8079 (mt0) cc_final: 0.7712 (mp10) REVERT: G 465 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8596 (mmm-85) REVERT: G 470 HIS cc_start: 0.8553 (m-70) cc_final: 0.8195 (m-70) REVERT: G 478 GLU cc_start: 0.8485 (pm20) cc_final: 0.8169 (pm20) REVERT: G 482 LYS cc_start: 0.8542 (tptp) cc_final: 0.8114 (tptp) REVERT: G 486 GLN cc_start: 0.7753 (mm110) cc_final: 0.7441 (mm110) REVERT: G 488 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7440 (tm) REVERT: G 495 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8146 (p) REVERT: G 497 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8630 (mm) REVERT: G 498 GLN cc_start: 0.8507 (tp40) cc_final: 0.8042 (tp40) REVERT: G 501 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8285 (ttp-170) REVERT: G 503 PHE cc_start: 0.8688 (t80) cc_final: 0.8294 (t80) REVERT: G 504 ILE cc_start: 0.8712 (mm) cc_final: 0.8401 (mm) REVERT: G 506 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7445 (mm-30) REVERT: G 510 ILE cc_start: 0.8167 (mm) cc_final: 0.7924 (mm) REVERT: G 518 LEU cc_start: 0.8093 (mt) cc_final: 0.7401 (pp) REVERT: G 554 MET cc_start: 0.6524 (tmm) cc_final: 0.5788 (tmm) REVERT: F 176 ASN cc_start: 0.8380 (t0) cc_final: 0.7835 (m-40) REVERT: F 191 ASP cc_start: 0.8641 (p0) cc_final: 0.8067 (p0) REVERT: F 192 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8226 (mmtt) REVERT: F 194 LEU cc_start: 0.8927 (mt) cc_final: 0.8464 (mm) REVERT: F 197 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7642 (ptp-170) REVERT: F 198 GLN cc_start: 0.8306 (pm20) cc_final: 0.7438 (tp40) REVERT: F 215 PHE cc_start: 0.6615 (m-80) cc_final: 0.6258 (m-80) REVERT: F 257 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7298 (tmmt) REVERT: F 277 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7874 (mtt) REVERT: F 322 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7124 (mt-10) REVERT: F 325 ASP cc_start: 0.7857 (m-30) cc_final: 0.7151 (m-30) REVERT: F 327 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8077 (mm-30) REVERT: F 333 MET cc_start: 0.7643 (tpp) cc_final: 0.7241 (mpp) REVERT: F 334 MET cc_start: 0.8217 (tpt) cc_final: 0.7231 (tpt) REVERT: F 338 LEU cc_start: 0.8878 (tp) cc_final: 0.8613 (mt) REVERT: F 346 MET cc_start: 0.7673 (mtt) cc_final: 0.6894 (mtt) REVERT: F 347 GLN cc_start: 0.8417 (tp-100) cc_final: 0.7628 (tp-100) REVERT: F 349 PHE cc_start: 0.8608 (t80) cc_final: 0.7948 (t80) REVERT: F 352 ASP cc_start: 0.8572 (t0) cc_final: 0.8290 (t70) REVERT: F 355 MET cc_start: 0.8199 (tpp) cc_final: 0.7310 (tpp) REVERT: F 357 ARG cc_start: 0.8455 (ttt180) cc_final: 0.8007 (ttt-90) REVERT: F 363 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8433 (mt) REVERT: F 366 THR cc_start: 0.8740 (t) cc_final: 0.8430 (p) REVERT: F 369 GLN cc_start: 0.6553 (tm-30) cc_final: 0.6182 (tm-30) REVERT: F 373 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7542 (ttp80) REVERT: F 374 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7737 (mm-40) REVERT: F 392 ILE cc_start: 0.7681 (tp) cc_final: 0.7339 (tp) REVERT: F 405 SER cc_start: 0.8755 (t) cc_final: 0.8499 (p) REVERT: F 423 PHE cc_start: 0.8614 (t80) cc_final: 0.8388 (t80) REVERT: F 429 GLN cc_start: 0.8732 (mt0) cc_final: 0.8384 (mt0) REVERT: F 435 TRP cc_start: 0.8248 (t60) cc_final: 0.8009 (t60) REVERT: F 437 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7786 (mm110) REVERT: F 446 GLU cc_start: 0.8490 (tt0) cc_final: 0.8099 (pt0) REVERT: F 448 GLN cc_start: 0.8826 (mt0) cc_final: 0.8289 (mt0) REVERT: F 464 GLU cc_start: 0.7783 (tp30) cc_final: 0.7299 (tp30) REVERT: F 495 SER cc_start: 0.8232 (t) cc_final: 0.7735 (p) REVERT: F 498 GLN cc_start: 0.8076 (tm-30) cc_final: 0.6797 (tp-100) REVERT: F 501 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.8109 (ttp80) REVERT: F 502 ASN cc_start: 0.7958 (t0) cc_final: 0.7508 (t0) REVERT: F 528 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.4747 (mtm180) REVERT: F 538 CYS cc_start: 0.8385 (m) cc_final: 0.7732 (m) REVERT: F 539 TYR cc_start: 0.7981 (t80) cc_final: 0.7347 (t80) REVERT: F 575 HIS cc_start: 0.8697 (m90) cc_final: 0.8407 (m90) REVERT: F 581 ASN cc_start: 0.8282 (t0) cc_final: 0.8053 (t0) REVERT: F 583 GLN cc_start: 0.8725 (mm110) cc_final: 0.8520 (mm110) REVERT: F 587 GLU cc_start: 0.8096 (tt0) cc_final: 0.7759 (tt0) REVERT: F 596 LEU cc_start: 0.7278 (mt) cc_final: 0.6999 (mt) REVERT: F 611 LYS cc_start: 0.8434 (pttt) cc_final: 0.8129 (pttt) REVERT: F 616 LEU cc_start: 0.8234 (tt) cc_final: 0.7972 (mm) REVERT: F 617 TRP cc_start: 0.8236 (t60) cc_final: 0.7869 (t60) REVERT: F 628 GLU cc_start: 0.8240 (pt0) cc_final: 0.7777 (pt0) REVERT: F 676 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: F 684 ASP cc_start: 0.8362 (t0) cc_final: 0.7743 (p0) outliers start: 43 outliers final: 25 residues processed: 398 average time/residue: 0.2477 time to fit residues: 121.5375 Evaluate side-chains 404 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 370 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 330 ARG Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 419 CYS Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ASN Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 597 GLN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN F 193 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN F 494 GLN F 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097332 restraints weight = 15372.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101167 restraints weight = 7820.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103720 restraints weight = 4764.721| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6998 Z= 0.191 Angle : 0.748 11.076 9480 Z= 0.374 Chirality : 0.046 0.255 1059 Planarity : 0.005 0.060 1227 Dihedral : 6.267 57.471 953 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 6.41 % Allowed : 27.24 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 835 helix: 1.05 (0.23), residues: 478 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 535 HIS 0.004 0.001 HIS F 364 PHE 0.013 0.001 PHE F 174 TYR 0.023 0.002 TYR F 546 ARG 0.010 0.001 ARG F 330 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 342) hydrogen bonds : angle 4.62696 ( 984) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.57746 ( 4) covalent geometry : bond 0.00386 ( 6996) covalent geometry : angle 0.74757 ( 9476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 383 time to evaluate : 0.823 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: G 181 LEU cc_start: 0.8492 (mp) cc_final: 0.7904 (pt) REVERT: G 182 SER cc_start: 0.8410 (p) cc_final: 0.7947 (t) REVERT: G 192 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8739 (mtpt) REVERT: G 201 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8173 (m) REVERT: G 204 ASP cc_start: 0.7709 (t70) cc_final: 0.7358 (t0) REVERT: G 223 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7846 (mtmm) REVERT: G 244 VAL cc_start: 0.8420 (m) cc_final: 0.8168 (p) REVERT: G 257 LYS cc_start: 0.8890 (mttt) cc_final: 0.8079 (mttm) REVERT: G 258 ARG cc_start: 0.6959 (mtt180) cc_final: 0.6710 (mtt180) REVERT: G 272 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (mm) REVERT: G 284 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8622 (tp) REVERT: G 288 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7102 (tpt170) REVERT: G 290 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7534 (mtp85) REVERT: G 293 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6790 (tm-30) REVERT: G 294 ARG cc_start: 0.6040 (tmt-80) cc_final: 0.5577 (tmt-80) REVERT: G 299 GLN cc_start: 0.8557 (mp10) cc_final: 0.8232 (mp10) REVERT: G 312 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7693 (tm-30) REVERT: G 318 LEU cc_start: 0.8854 (tp) cc_final: 0.8452 (tp) REVERT: G 327 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7919 (tm-30) REVERT: G 342 GLU cc_start: 0.7930 (mp0) cc_final: 0.7410 (mp0) REVERT: G 344 GLU cc_start: 0.8278 (tp30) cc_final: 0.7048 (tp30) REVERT: G 348 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8454 (mmt90) REVERT: G 349 PHE cc_start: 0.9002 (t80) cc_final: 0.8600 (t80) REVERT: G 355 MET cc_start: 0.7771 (tpp) cc_final: 0.6806 (tpp) REVERT: G 359 LEU cc_start: 0.9054 (mt) cc_final: 0.8356 (mm) REVERT: G 408 LYS cc_start: 0.8285 (tppt) cc_final: 0.7655 (tppt) REVERT: G 412 ARG cc_start: 0.8570 (ttt180) cc_final: 0.7963 (ttp-170) REVERT: G 417 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8350 (mtm-85) REVERT: G 419 CYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8304 (m) REVERT: G 420 VAL cc_start: 0.9071 (p) cc_final: 0.8714 (p) REVERT: G 421 TYR cc_start: 0.8232 (t80) cc_final: 0.7664 (t80) REVERT: G 423 PHE cc_start: 0.8599 (t80) cc_final: 0.8291 (t80) REVERT: G 424 LEU cc_start: 0.8949 (mt) cc_final: 0.8697 (mt) REVERT: G 425 CYS cc_start: 0.8876 (m) cc_final: 0.8480 (m) REVERT: G 426 TYR cc_start: 0.8493 (t80) cc_final: 0.8279 (t80) REVERT: G 428 TRP cc_start: 0.8761 (t-100) cc_final: 0.8559 (t-100) REVERT: G 429 GLN cc_start: 0.8310 (tt0) cc_final: 0.7966 (tt0) REVERT: G 432 MET cc_start: 0.7966 (mmm) cc_final: 0.7402 (mmm) REVERT: G 443 ASN cc_start: 0.8664 (m110) cc_final: 0.8184 (m110) REVERT: G 444 LEU cc_start: 0.8829 (mm) cc_final: 0.8612 (mm) REVERT: G 445 LYS cc_start: 0.8784 (mptp) cc_final: 0.8382 (mptp) REVERT: G 446 GLU cc_start: 0.7670 (tt0) cc_final: 0.7195 (pt0) REVERT: G 448 GLN cc_start: 0.8426 (mt0) cc_final: 0.7316 (mt0) REVERT: G 452 LYS cc_start: 0.8608 (mttm) cc_final: 0.7952 (mttm) REVERT: G 453 GLN cc_start: 0.8206 (mt0) cc_final: 0.7805 (mp10) REVERT: G 455 LEU cc_start: 0.8918 (tp) cc_final: 0.8670 (tp) REVERT: G 458 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (mm) REVERT: G 478 GLU cc_start: 0.8503 (pm20) cc_final: 0.8151 (pm20) REVERT: G 482 LYS cc_start: 0.8563 (tptp) cc_final: 0.7928 (tptp) REVERT: G 483 THR cc_start: 0.8866 (t) cc_final: 0.8612 (p) REVERT: G 485 GLN cc_start: 0.8358 (mt0) cc_final: 0.8114 (mt0) REVERT: G 495 SER cc_start: 0.8830 (m) cc_final: 0.8240 (p) REVERT: G 497 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8557 (mm) REVERT: G 498 GLN cc_start: 0.8665 (tp40) cc_final: 0.7487 (tp40) REVERT: G 501 ARG cc_start: 0.8678 (ttp-170) cc_final: 0.8043 (ptp-110) REVERT: G 502 ASN cc_start: 0.8260 (t0) cc_final: 0.7197 (t0) REVERT: G 504 ILE cc_start: 0.8706 (mm) cc_final: 0.8396 (mm) REVERT: G 506 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 507 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8263 (mmm160) REVERT: G 540 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8429 (mm) REVERT: G 547 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8751 (mm) REVERT: G 554 MET cc_start: 0.6716 (tmm) cc_final: 0.6088 (tmm) REVERT: F 167 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5685 (mp) REVERT: F 175 GLN cc_start: 0.7360 (tm130) cc_final: 0.7120 (tm-30) REVERT: F 178 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8165 (mmmt) REVERT: F 191 ASP cc_start: 0.8600 (p0) cc_final: 0.7911 (p0) REVERT: F 192 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8094 (mmtt) REVERT: F 193 GLN cc_start: 0.8763 (mm110) cc_final: 0.8470 (mm-40) REVERT: F 194 LEU cc_start: 0.8840 (mt) cc_final: 0.8565 (mm) REVERT: F 198 GLN cc_start: 0.8368 (pm20) cc_final: 0.7663 (tp40) REVERT: F 215 PHE cc_start: 0.6698 (m-80) cc_final: 0.6363 (m-80) REVERT: F 277 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: F 313 GLN cc_start: 0.8676 (mp-120) cc_final: 0.7906 (pt0) REVERT: F 322 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7178 (mt-10) REVERT: F 325 ASP cc_start: 0.7953 (m-30) cc_final: 0.7167 (m-30) REVERT: F 327 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7899 (mm-30) REVERT: F 333 MET cc_start: 0.7932 (tpp) cc_final: 0.7511 (mpp) REVERT: F 334 MET cc_start: 0.8247 (tpt) cc_final: 0.7932 (tpt) REVERT: F 346 MET cc_start: 0.7728 (mtt) cc_final: 0.6989 (mtt) REVERT: F 349 PHE cc_start: 0.8643 (t80) cc_final: 0.8125 (t80) REVERT: F 355 MET cc_start: 0.8250 (tpp) cc_final: 0.7340 (tpp) REVERT: F 356 GLN cc_start: 0.8449 (tt0) cc_final: 0.7904 (tm-30) REVERT: F 357 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8023 (ttt-90) REVERT: F 358 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8053 (mtpp) REVERT: F 363 LEU cc_start: 0.8813 (mm) cc_final: 0.8460 (mt) REVERT: F 369 GLN cc_start: 0.6539 (tm-30) cc_final: 0.5816 (tm-30) REVERT: F 373 ARG cc_start: 0.8127 (ttt180) cc_final: 0.7681 (ttp80) REVERT: F 374 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7793 (mm-40) REVERT: F 383 LEU cc_start: 0.8516 (mm) cc_final: 0.8264 (mt) REVERT: F 405 SER cc_start: 0.8741 (t) cc_final: 0.8493 (p) REVERT: F 419 CYS cc_start: 0.8846 (m) cc_final: 0.8329 (p) REVERT: F 423 PHE cc_start: 0.8680 (t80) cc_final: 0.8355 (t80) REVERT: F 429 GLN cc_start: 0.8725 (mt0) cc_final: 0.8369 (mt0) REVERT: F 437 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7802 (mm110) REVERT: F 446 GLU cc_start: 0.8489 (tt0) cc_final: 0.7945 (pt0) REVERT: F 448 GLN cc_start: 0.8832 (mt0) cc_final: 0.8281 (mt0) REVERT: F 464 GLU cc_start: 0.7982 (tp30) cc_final: 0.7414 (tp30) REVERT: F 485 GLN cc_start: 0.7491 (mt0) cc_final: 0.7198 (pt0) REVERT: F 495 SER cc_start: 0.7960 (t) cc_final: 0.7229 (p) REVERT: F 498 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7734 (tp-100) REVERT: F 502 ASN cc_start: 0.7974 (t0) cc_final: 0.6959 (t0) REVERT: F 506 GLU cc_start: 0.7547 (pt0) cc_final: 0.6765 (pt0) REVERT: F 528 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.5222 (ttp-170) REVERT: F 538 CYS cc_start: 0.8455 (m) cc_final: 0.7847 (m) REVERT: F 539 TYR cc_start: 0.8101 (t80) cc_final: 0.7363 (t80) REVERT: F 575 HIS cc_start: 0.8762 (m90) cc_final: 0.8485 (m90) REVERT: F 576 ARG cc_start: 0.7538 (mmp80) cc_final: 0.7134 (mtm-85) REVERT: F 581 ASN cc_start: 0.8307 (t0) cc_final: 0.7919 (t0) REVERT: F 583 GLN cc_start: 0.8780 (mm110) cc_final: 0.8555 (mm110) REVERT: F 587 GLU cc_start: 0.8168 (tt0) cc_final: 0.7829 (tt0) REVERT: F 611 LYS cc_start: 0.8516 (pttt) cc_final: 0.8060 (mmtp) REVERT: F 616 LEU cc_start: 0.8211 (tt) cc_final: 0.7981 (mm) REVERT: F 617 TRP cc_start: 0.8256 (t60) cc_final: 0.7830 (t60) REVERT: F 621 TYR cc_start: 0.8643 (t80) cc_final: 0.8224 (t80) REVERT: F 623 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7568 (ttp80) REVERT: F 628 GLU cc_start: 0.8286 (pt0) cc_final: 0.7791 (pt0) REVERT: F 637 PHE cc_start: 0.8305 (m-80) cc_final: 0.8072 (m-80) REVERT: F 672 GLU cc_start: 0.8306 (pp20) cc_final: 0.7921 (pp20) REVERT: F 676 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7860 (ttm-80) REVERT: F 684 ASP cc_start: 0.8258 (t0) cc_final: 0.7406 (t0) REVERT: F 686 GLN cc_start: 0.8056 (pm20) cc_final: 0.7813 (pm20) outliers start: 48 outliers final: 17 residues processed: 402 average time/residue: 0.2301 time to fit residues: 115.4810 Evaluate side-chains 406 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 419 CYS Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 396 ASN Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 12 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 186 ASN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN F 463 ASN F 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.116804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098136 restraints weight = 15411.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101928 restraints weight = 7880.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104501 restraints weight = 4832.769| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6998 Z= 0.171 Angle : 0.734 12.692 9480 Z= 0.364 Chirality : 0.046 0.205 1059 Planarity : 0.005 0.044 1227 Dihedral : 5.041 52.249 938 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.41 % Allowed : 28.97 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.30), residues: 835 helix: 1.18 (0.24), residues: 477 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 535 HIS 0.005 0.001 HIS F 633 PHE 0.016 0.001 PHE G 503 TYR 0.023 0.002 TYR F 546 ARG 0.009 0.001 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 342) hydrogen bonds : angle 4.52899 ( 984) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.53695 ( 4) covalent geometry : bond 0.00354 ( 6996) covalent geometry : angle 0.73379 ( 9476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.817 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LEU cc_start: 0.8491 (mp) cc_final: 0.7886 (pt) REVERT: G 182 SER cc_start: 0.8378 (p) cc_final: 0.7926 (t) REVERT: G 193 GLN cc_start: 0.8740 (mp10) cc_final: 0.8315 (mp10) REVERT: G 201 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8151 (m) REVERT: G 204 ASP cc_start: 0.7769 (t70) cc_final: 0.7430 (t0) REVERT: G 223 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7893 (mtmm) REVERT: G 257 LYS cc_start: 0.8917 (mttt) cc_final: 0.8336 (mttm) REVERT: G 258 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6641 (mtt180) REVERT: G 272 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8868 (mm) REVERT: G 277 MET cc_start: 0.8145 (mmm) cc_final: 0.7613 (mmm) REVERT: G 288 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7236 (tpt-90) REVERT: G 290 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7538 (mtp85) REVERT: G 293 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6892 (tm-30) REVERT: G 294 ARG cc_start: 0.6149 (tmt-80) cc_final: 0.5405 (tmt170) REVERT: G 299 GLN cc_start: 0.8543 (mp10) cc_final: 0.8211 (mp10) REVERT: G 312 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 314 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8263 (pp) REVERT: G 318 LEU cc_start: 0.8880 (tp) cc_final: 0.8472 (tp) REVERT: G 327 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7965 (tm-30) REVERT: G 342 GLU cc_start: 0.7869 (mp0) cc_final: 0.7342 (mp0) REVERT: G 344 GLU cc_start: 0.8270 (tp30) cc_final: 0.6839 (tp30) REVERT: G 347 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8471 (tm-30) REVERT: G 348 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8325 (mmt90) REVERT: G 349 PHE cc_start: 0.8983 (t80) cc_final: 0.8597 (t80) REVERT: G 355 MET cc_start: 0.7897 (tpp) cc_final: 0.6951 (tpp) REVERT: G 359 LEU cc_start: 0.9057 (mt) cc_final: 0.8411 (mm) REVERT: G 417 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8366 (mtm-85) REVERT: G 419 CYS cc_start: 0.8671 (m) cc_final: 0.8170 (m) REVERT: G 421 TYR cc_start: 0.8205 (t80) cc_final: 0.7579 (t80) REVERT: G 422 LEU cc_start: 0.8763 (mt) cc_final: 0.8532 (mt) REVERT: G 423 PHE cc_start: 0.8620 (t80) cc_final: 0.8278 (t80) REVERT: G 424 LEU cc_start: 0.8918 (mt) cc_final: 0.8659 (mt) REVERT: G 425 CYS cc_start: 0.8847 (m) cc_final: 0.8469 (m) REVERT: G 426 TYR cc_start: 0.8543 (t80) cc_final: 0.8282 (t80) REVERT: G 429 GLN cc_start: 0.8311 (tt0) cc_final: 0.7975 (tt0) REVERT: G 432 MET cc_start: 0.7922 (mmm) cc_final: 0.7372 (mmm) REVERT: G 442 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7415 (mtp-110) REVERT: G 445 LYS cc_start: 0.8761 (mptp) cc_final: 0.8323 (mptp) REVERT: G 446 GLU cc_start: 0.7610 (tt0) cc_final: 0.7128 (pt0) REVERT: G 448 GLN cc_start: 0.8442 (mt0) cc_final: 0.7299 (mt0) REVERT: G 449 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7593 (mmmm) REVERT: G 452 LYS cc_start: 0.8665 (mttm) cc_final: 0.7959 (mttm) REVERT: G 453 GLN cc_start: 0.8263 (mt0) cc_final: 0.7848 (mp10) REVERT: G 455 LEU cc_start: 0.8833 (tp) cc_final: 0.8596 (tp) REVERT: G 456 LYS cc_start: 0.9259 (tmtm) cc_final: 0.8869 (tmtm) REVERT: G 458 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8109 (mm) REVERT: G 478 GLU cc_start: 0.8530 (pm20) cc_final: 0.8159 (pm20) REVERT: G 482 LYS cc_start: 0.8567 (tptp) cc_final: 0.7837 (tptp) REVERT: G 495 SER cc_start: 0.8841 (m) cc_final: 0.8212 (p) REVERT: G 497 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8562 (mm) REVERT: G 498 GLN cc_start: 0.8658 (tp40) cc_final: 0.7492 (tp40) REVERT: G 501 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8005 (ptp-110) REVERT: G 502 ASN cc_start: 0.8190 (t0) cc_final: 0.7197 (t0) REVERT: G 504 ILE cc_start: 0.8686 (mm) cc_final: 0.8401 (mm) REVERT: G 506 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7539 (mm-30) REVERT: G 507 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8127 (mmm160) REVERT: G 540 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8450 (mm) REVERT: F 167 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5697 (mp) REVERT: F 175 GLN cc_start: 0.7371 (tm130) cc_final: 0.6987 (tm-30) REVERT: F 178 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8097 (mmpt) REVERT: F 191 ASP cc_start: 0.8572 (p0) cc_final: 0.7869 (p0) REVERT: F 192 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8016 (mmtt) REVERT: F 193 GLN cc_start: 0.8746 (mm110) cc_final: 0.8382 (mm110) REVERT: F 194 LEU cc_start: 0.8796 (mt) cc_final: 0.8519 (mm) REVERT: F 198 GLN cc_start: 0.8354 (pm20) cc_final: 0.7667 (tp40) REVERT: F 204 ASP cc_start: 0.8202 (p0) cc_final: 0.7975 (p0) REVERT: F 215 PHE cc_start: 0.6736 (m-80) cc_final: 0.6403 (m-80) REVERT: F 277 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7473 (mtt) REVERT: F 281 MET cc_start: 0.6986 (mmt) cc_final: 0.6776 (mmt) REVERT: F 313 GLN cc_start: 0.8552 (mp-120) cc_final: 0.8225 (pt0) REVERT: F 322 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7097 (mt-10) REVERT: F 325 ASP cc_start: 0.8013 (m-30) cc_final: 0.7427 (m-30) REVERT: F 327 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7875 (mm-30) REVERT: F 330 ARG cc_start: 0.8225 (ptt90) cc_final: 0.8016 (ptt90) REVERT: F 333 MET cc_start: 0.7757 (tpp) cc_final: 0.7481 (mpp) REVERT: F 334 MET cc_start: 0.8185 (tpt) cc_final: 0.7850 (tpt) REVERT: F 346 MET cc_start: 0.7699 (mtt) cc_final: 0.6890 (mtt) REVERT: F 349 PHE cc_start: 0.8636 (t80) cc_final: 0.7851 (t80) REVERT: F 355 MET cc_start: 0.8256 (tpp) cc_final: 0.7320 (tpp) REVERT: F 356 GLN cc_start: 0.8544 (tt0) cc_final: 0.8013 (tm-30) REVERT: F 357 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8050 (ttt-90) REVERT: F 358 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8106 (mtpp) REVERT: F 363 LEU cc_start: 0.8799 (mm) cc_final: 0.8450 (mt) REVERT: F 368 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7276 (ttt-90) REVERT: F 369 GLN cc_start: 0.6707 (tm-30) cc_final: 0.5901 (tm-30) REVERT: F 373 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7716 (ttp80) REVERT: F 374 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7823 (mm-40) REVERT: F 394 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: F 405 SER cc_start: 0.8802 (t) cc_final: 0.8587 (p) REVERT: F 419 CYS cc_start: 0.8816 (m) cc_final: 0.8361 (p) REVERT: F 423 PHE cc_start: 0.8642 (t80) cc_final: 0.8361 (t80) REVERT: F 437 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: F 441 GLU cc_start: 0.8010 (mp0) cc_final: 0.7741 (tp30) REVERT: F 446 GLU cc_start: 0.8500 (tt0) cc_final: 0.7949 (pt0) REVERT: F 464 GLU cc_start: 0.7826 (tp30) cc_final: 0.7519 (tp30) REVERT: F 482 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8212 (mmtp) REVERT: F 485 GLN cc_start: 0.7609 (mt0) cc_final: 0.7334 (mt0) REVERT: F 495 SER cc_start: 0.8099 (t) cc_final: 0.7309 (p) REVERT: F 498 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7940 (tp-100) REVERT: F 499 ASN cc_start: 0.8365 (m-40) cc_final: 0.7988 (m110) REVERT: F 502 ASN cc_start: 0.8004 (t0) cc_final: 0.6880 (t0) REVERT: F 506 GLU cc_start: 0.7528 (pt0) cc_final: 0.6599 (pt0) REVERT: F 528 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.4946 (ttp-170) REVERT: F 539 TYR cc_start: 0.8152 (t80) cc_final: 0.7458 (t80) REVERT: F 575 HIS cc_start: 0.8741 (m90) cc_final: 0.8454 (m90) REVERT: F 576 ARG cc_start: 0.7526 (mmp80) cc_final: 0.7056 (mtm-85) REVERT: F 581 ASN cc_start: 0.8312 (t0) cc_final: 0.7896 (t0) REVERT: F 583 GLN cc_start: 0.8787 (mm110) cc_final: 0.8554 (mm110) REVERT: F 587 GLU cc_start: 0.8243 (tt0) cc_final: 0.7907 (tt0) REVERT: F 611 LYS cc_start: 0.8606 (pttt) cc_final: 0.8159 (mmtp) REVERT: F 616 LEU cc_start: 0.8213 (tt) cc_final: 0.7960 (mm) REVERT: F 617 TRP cc_start: 0.8278 (t60) cc_final: 0.7852 (t60) REVERT: F 621 TYR cc_start: 0.8610 (t80) cc_final: 0.8188 (t80) REVERT: F 623 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7680 (ttp80) REVERT: F 628 GLU cc_start: 0.8273 (pt0) cc_final: 0.7811 (pt0) REVERT: F 637 PHE cc_start: 0.8319 (m-80) cc_final: 0.8103 (m-80) REVERT: F 672 GLU cc_start: 0.8269 (pp20) cc_final: 0.7871 (pp20) REVERT: F 676 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: F 684 ASP cc_start: 0.8274 (t0) cc_final: 0.7895 (t0) outliers start: 48 outliers final: 28 residues processed: 404 average time/residue: 0.3434 time to fit residues: 173.9304 Evaluate side-chains 418 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 378 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 650 THR Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 664 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 8 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 443 ASN ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN F 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099330 restraints weight = 15102.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103049 restraints weight = 7718.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105565 restraints weight = 4752.567| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6998 Z= 0.137 Angle : 0.725 11.149 9480 Z= 0.357 Chirality : 0.044 0.211 1059 Planarity : 0.004 0.036 1227 Dihedral : 4.842 52.915 936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.01 % Allowed : 32.71 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.30), residues: 835 helix: 1.35 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 459 HIS 0.005 0.001 HIS F 633 PHE 0.021 0.001 PHE G 503 TYR 0.024 0.001 TYR F 546 ARG 0.009 0.001 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 342) hydrogen bonds : angle 4.49203 ( 984) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.64260 ( 4) covalent geometry : bond 0.00298 ( 6996) covalent geometry : angle 0.72486 ( 9476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 383 time to evaluate : 0.802 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LEU cc_start: 0.8474 (mp) cc_final: 0.7846 (pt) REVERT: G 182 SER cc_start: 0.8364 (p) cc_final: 0.7908 (t) REVERT: G 193 GLN cc_start: 0.8737 (mp10) cc_final: 0.8264 (mp10) REVERT: G 201 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8125 (m) REVERT: G 204 ASP cc_start: 0.7652 (t70) cc_final: 0.7283 (t0) REVERT: G 223 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7898 (mtmm) REVERT: G 257 LYS cc_start: 0.8867 (mttt) cc_final: 0.8326 (mttm) REVERT: G 258 ARG cc_start: 0.6928 (mtt180) cc_final: 0.6614 (mtt180) REVERT: G 272 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8855 (mm) REVERT: G 277 MET cc_start: 0.8116 (mmm) cc_final: 0.7624 (mmm) REVERT: G 288 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7222 (tpt170) REVERT: G 290 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7539 (mtp85) REVERT: G 293 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6954 (tm-30) REVERT: G 294 ARG cc_start: 0.6105 (tmt-80) cc_final: 0.4893 (tmt-80) REVERT: G 299 GLN cc_start: 0.8536 (mp10) cc_final: 0.8251 (mp10) REVERT: G 312 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7758 (tm-30) REVERT: G 314 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8250 (pp) REVERT: G 318 LEU cc_start: 0.8916 (tp) cc_final: 0.8521 (tp) REVERT: G 327 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7991 (tm-30) REVERT: G 342 GLU cc_start: 0.7855 (mp0) cc_final: 0.7341 (mp0) REVERT: G 344 GLU cc_start: 0.8222 (tp30) cc_final: 0.6893 (tp30) REVERT: G 348 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8185 (mmt90) REVERT: G 349 PHE cc_start: 0.8963 (t80) cc_final: 0.8577 (t80) REVERT: G 355 MET cc_start: 0.7904 (tpp) cc_final: 0.6949 (tpp) REVERT: G 359 LEU cc_start: 0.8982 (mt) cc_final: 0.8397 (mm) REVERT: G 408 LYS cc_start: 0.8406 (tppt) cc_final: 0.8087 (tppt) REVERT: G 412 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8027 (ttp-170) REVERT: G 417 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8419 (mtm-85) REVERT: G 419 CYS cc_start: 0.8692 (m) cc_final: 0.8219 (m) REVERT: G 423 PHE cc_start: 0.8614 (t80) cc_final: 0.8280 (t80) REVERT: G 424 LEU cc_start: 0.8898 (mt) cc_final: 0.8691 (mt) REVERT: G 425 CYS cc_start: 0.8807 (m) cc_final: 0.8467 (m) REVERT: G 426 TYR cc_start: 0.8533 (t80) cc_final: 0.8297 (t80) REVERT: G 428 TRP cc_start: 0.8657 (t-100) cc_final: 0.8453 (t-100) REVERT: G 429 GLN cc_start: 0.8339 (tt0) cc_final: 0.8005 (tt0) REVERT: G 432 MET cc_start: 0.7863 (mmm) cc_final: 0.7301 (mmm) REVERT: G 443 ASN cc_start: 0.8478 (m-40) cc_final: 0.7515 (m-40) REVERT: G 445 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8313 (mptp) REVERT: G 446 GLU cc_start: 0.7776 (tt0) cc_final: 0.7332 (pt0) REVERT: G 448 GLN cc_start: 0.8406 (mt0) cc_final: 0.7294 (mt0) REVERT: G 449 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7580 (mmmm) REVERT: G 452 LYS cc_start: 0.8630 (mttm) cc_final: 0.7900 (mttm) REVERT: G 453 GLN cc_start: 0.8251 (mt0) cc_final: 0.7870 (mp10) REVERT: G 455 LEU cc_start: 0.8843 (tp) cc_final: 0.8619 (tp) REVERT: G 456 LYS cc_start: 0.9258 (tmtm) cc_final: 0.8828 (tmtm) REVERT: G 458 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8045 (mm) REVERT: G 478 GLU cc_start: 0.8483 (pm20) cc_final: 0.8116 (pm20) REVERT: G 482 LYS cc_start: 0.8507 (tptp) cc_final: 0.7877 (tptp) REVERT: G 495 SER cc_start: 0.8780 (m) cc_final: 0.8248 (p) REVERT: G 497 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8567 (mm) REVERT: G 498 GLN cc_start: 0.8653 (tp40) cc_final: 0.7596 (tp40) REVERT: G 501 ARG cc_start: 0.8659 (ttp-170) cc_final: 0.7953 (ptp-110) REVERT: G 502 ASN cc_start: 0.8169 (t0) cc_final: 0.7168 (t0) REVERT: G 504 ILE cc_start: 0.8685 (mm) cc_final: 0.8397 (mm) REVERT: G 506 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7453 (mm-30) REVERT: G 507 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8067 (mmm160) REVERT: G 522 PHE cc_start: 0.8547 (m-80) cc_final: 0.8338 (m-10) REVERT: G 540 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (mm) REVERT: F 175 GLN cc_start: 0.7400 (tm130) cc_final: 0.6740 (tm-30) REVERT: F 178 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8178 (mmmt) REVERT: F 191 ASP cc_start: 0.8482 (p0) cc_final: 0.8002 (p0) REVERT: F 192 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8034 (mmtt) REVERT: F 193 GLN cc_start: 0.8651 (mm110) cc_final: 0.8303 (mm110) REVERT: F 194 LEU cc_start: 0.8780 (mt) cc_final: 0.8483 (mm) REVERT: F 198 GLN cc_start: 0.8312 (pm20) cc_final: 0.7600 (tp40) REVERT: F 215 PHE cc_start: 0.6701 (m-80) cc_final: 0.6375 (m-80) REVERT: F 277 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7462 (mtt) REVERT: F 281 MET cc_start: 0.6980 (mmt) cc_final: 0.6751 (mmt) REVERT: F 284 LEU cc_start: 0.6669 (mt) cc_final: 0.5952 (tt) REVERT: F 313 GLN cc_start: 0.8680 (mp10) cc_final: 0.8252 (pt0) REVERT: F 316 ARG cc_start: 0.7244 (mmp80) cc_final: 0.7016 (mmp80) REVERT: F 322 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 325 ASP cc_start: 0.7968 (m-30) cc_final: 0.7466 (m-30) REVERT: F 327 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8052 (mm-30) REVERT: F 330 ARG cc_start: 0.8186 (ptt90) cc_final: 0.7935 (ptt90) REVERT: F 333 MET cc_start: 0.7830 (tpp) cc_final: 0.7500 (mpp) REVERT: F 334 MET cc_start: 0.8187 (tpt) cc_final: 0.7826 (tpt) REVERT: F 346 MET cc_start: 0.7701 (mtt) cc_final: 0.7102 (mtt) REVERT: F 349 PHE cc_start: 0.8663 (t80) cc_final: 0.7871 (t80) REVERT: F 355 MET cc_start: 0.8183 (tpp) cc_final: 0.7289 (tpp) REVERT: F 356 GLN cc_start: 0.8535 (tt0) cc_final: 0.7973 (tm-30) REVERT: F 357 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8013 (ttt-90) REVERT: F 358 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8098 (mtpp) REVERT: F 369 GLN cc_start: 0.6786 (tm-30) cc_final: 0.5882 (tm-30) REVERT: F 373 ARG cc_start: 0.8201 (ttt180) cc_final: 0.7727 (ttp80) REVERT: F 394 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6900 (t-90) REVERT: F 405 SER cc_start: 0.8706 (t) cc_final: 0.8463 (p) REVERT: F 419 CYS cc_start: 0.8858 (m) cc_final: 0.8356 (p) REVERT: F 423 PHE cc_start: 0.8592 (t80) cc_final: 0.8289 (t80) REVERT: F 437 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7770 (mm110) REVERT: F 448 GLN cc_start: 0.8815 (mt0) cc_final: 0.8249 (mt0) REVERT: F 464 GLU cc_start: 0.7811 (tp30) cc_final: 0.7522 (tp30) REVERT: F 482 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8202 (mmtp) REVERT: F 485 GLN cc_start: 0.7584 (mt0) cc_final: 0.7344 (mt0) REVERT: F 495 SER cc_start: 0.7973 (t) cc_final: 0.7138 (p) REVERT: F 498 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7952 (tp-100) REVERT: F 499 ASN cc_start: 0.8302 (m-40) cc_final: 0.7852 (m110) REVERT: F 502 ASN cc_start: 0.7866 (t0) cc_final: 0.7375 (t0) REVERT: F 505 LEU cc_start: 0.8670 (mm) cc_final: 0.8459 (mm) REVERT: F 528 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.5574 (mtm110) REVERT: F 538 CYS cc_start: 0.8310 (m) cc_final: 0.7669 (m) REVERT: F 539 TYR cc_start: 0.8108 (t80) cc_final: 0.7530 (t80) REVERT: F 575 HIS cc_start: 0.8759 (m90) cc_final: 0.8465 (m90) REVERT: F 576 ARG cc_start: 0.7518 (mmp80) cc_final: 0.7045 (mtm-85) REVERT: F 581 ASN cc_start: 0.8272 (t0) cc_final: 0.7846 (t0) REVERT: F 583 GLN cc_start: 0.8779 (mm110) cc_final: 0.8544 (mm110) REVERT: F 587 GLU cc_start: 0.8220 (tt0) cc_final: 0.7845 (tt0) REVERT: F 596 LEU cc_start: 0.7852 (mt) cc_final: 0.7638 (mt) REVERT: F 611 LYS cc_start: 0.8534 (pttt) cc_final: 0.8319 (pttt) REVERT: F 616 LEU cc_start: 0.8214 (tt) cc_final: 0.7950 (mm) REVERT: F 617 TRP cc_start: 0.8319 (t60) cc_final: 0.7884 (t60) REVERT: F 621 TYR cc_start: 0.8567 (t80) cc_final: 0.8160 (t80) REVERT: F 623 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7555 (ttp80) REVERT: F 628 GLU cc_start: 0.8282 (pt0) cc_final: 0.7817 (pt0) REVERT: F 637 PHE cc_start: 0.8290 (m-80) cc_final: 0.8077 (m-80) REVERT: F 672 GLU cc_start: 0.8234 (pp20) cc_final: 0.7821 (pp20) REVERT: F 676 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: F 684 ASP cc_start: 0.8348 (t0) cc_final: 0.8067 (t0) outliers start: 45 outliers final: 29 residues processed: 397 average time/residue: 0.3268 time to fit residues: 165.5652 Evaluate side-chains 424 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 664 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 ASN F 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099027 restraints weight = 15339.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102821 restraints weight = 7829.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105380 restraints weight = 4776.672| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6998 Z= 0.134 Angle : 0.732 14.531 9480 Z= 0.357 Chirality : 0.044 0.187 1059 Planarity : 0.004 0.037 1227 Dihedral : 4.770 53.317 936 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 7.34 % Allowed : 32.31 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 835 helix: 1.43 (0.24), residues: 473 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 459 HIS 0.005 0.001 HIS F 633 PHE 0.013 0.001 PHE F 174 TYR 0.026 0.001 TYR F 546 ARG 0.008 0.001 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 342) hydrogen bonds : angle 4.46583 ( 984) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.63752 ( 4) covalent geometry : bond 0.00295 ( 6996) covalent geometry : angle 0.73228 ( 9476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 379 time to evaluate : 0.886 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LEU cc_start: 0.8477 (mp) cc_final: 0.7840 (pt) REVERT: G 182 SER cc_start: 0.8366 (p) cc_final: 0.7898 (t) REVERT: G 193 GLN cc_start: 0.8733 (mp10) cc_final: 0.8240 (mp10) REVERT: G 201 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (m) REVERT: G 204 ASP cc_start: 0.7630 (t70) cc_final: 0.7238 (t0) REVERT: G 223 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7909 (mtmm) REVERT: G 257 LYS cc_start: 0.8914 (mttt) cc_final: 0.8271 (mttt) REVERT: G 258 ARG cc_start: 0.6924 (mtt180) cc_final: 0.6571 (mtt180) REVERT: G 272 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8819 (mm) REVERT: G 277 MET cc_start: 0.8105 (mmm) cc_final: 0.7647 (mmm) REVERT: G 288 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7246 (tpt170) REVERT: G 290 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7594 (mtp85) REVERT: G 293 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6987 (tm-30) REVERT: G 294 ARG cc_start: 0.6247 (tmt-80) cc_final: 0.5034 (tmt-80) REVERT: G 299 GLN cc_start: 0.8535 (mp10) cc_final: 0.8318 (mp10) REVERT: G 312 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7784 (tm-30) REVERT: G 314 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8257 (pp) REVERT: G 318 LEU cc_start: 0.8878 (tp) cc_final: 0.8472 (tp) REVERT: G 327 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8001 (tm-30) REVERT: G 342 GLU cc_start: 0.7872 (mp0) cc_final: 0.7338 (mp0) REVERT: G 344 GLU cc_start: 0.8216 (tp30) cc_final: 0.6973 (tp30) REVERT: G 349 PHE cc_start: 0.8928 (t80) cc_final: 0.8568 (t80) REVERT: G 355 MET cc_start: 0.7979 (tpp) cc_final: 0.6999 (tpp) REVERT: G 359 LEU cc_start: 0.8988 (mt) cc_final: 0.8421 (mm) REVERT: G 412 ARG cc_start: 0.8524 (ttt180) cc_final: 0.7826 (ttt-90) REVERT: G 417 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8404 (mtm-85) REVERT: G 419 CYS cc_start: 0.8661 (m) cc_final: 0.8085 (m) REVERT: G 423 PHE cc_start: 0.8602 (t80) cc_final: 0.8271 (t80) REVERT: G 424 LEU cc_start: 0.8909 (mt) cc_final: 0.8697 (mt) REVERT: G 425 CYS cc_start: 0.8767 (m) cc_final: 0.8422 (m) REVERT: G 426 TYR cc_start: 0.8585 (t80) cc_final: 0.8356 (t80) REVERT: G 429 GLN cc_start: 0.8400 (tt0) cc_final: 0.8024 (tt0) REVERT: G 432 MET cc_start: 0.7886 (mmm) cc_final: 0.7292 (mmm) REVERT: G 443 ASN cc_start: 0.8445 (m-40) cc_final: 0.7548 (m-40) REVERT: G 445 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8330 (mptp) REVERT: G 446 GLU cc_start: 0.7758 (tt0) cc_final: 0.7310 (pt0) REVERT: G 448 GLN cc_start: 0.8386 (mt0) cc_final: 0.7273 (mt0) REVERT: G 449 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7580 (mmmm) REVERT: G 452 LYS cc_start: 0.8587 (mttm) cc_final: 0.7902 (mttm) REVERT: G 453 GLN cc_start: 0.8278 (mt0) cc_final: 0.7900 (mp10) REVERT: G 456 LYS cc_start: 0.9248 (tmtm) cc_final: 0.8819 (tmtm) REVERT: G 458 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7994 (mm) REVERT: G 478 GLU cc_start: 0.8486 (pm20) cc_final: 0.8134 (pm20) REVERT: G 482 LYS cc_start: 0.8502 (tptp) cc_final: 0.7823 (tptp) REVERT: G 495 SER cc_start: 0.8760 (m) cc_final: 0.8261 (p) REVERT: G 497 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8573 (mm) REVERT: G 498 GLN cc_start: 0.8637 (tp40) cc_final: 0.7709 (tp40) REVERT: G 501 ARG cc_start: 0.8650 (ttp-170) cc_final: 0.7952 (ptp-110) REVERT: G 502 ASN cc_start: 0.8171 (t0) cc_final: 0.7181 (t0) REVERT: G 504 ILE cc_start: 0.8685 (mm) cc_final: 0.8390 (mm) REVERT: G 506 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7459 (mm-30) REVERT: G 507 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8064 (mmm160) REVERT: G 522 PHE cc_start: 0.8553 (m-80) cc_final: 0.8343 (m-10) REVERT: G 540 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8474 (mm) REVERT: F 167 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5937 (pt) REVERT: F 173 PHE cc_start: 0.7937 (m-80) cc_final: 0.7587 (m-80) REVERT: F 175 GLN cc_start: 0.7405 (tm130) cc_final: 0.7067 (tm-30) REVERT: F 176 ASN cc_start: 0.8286 (t0) cc_final: 0.7969 (m110) REVERT: F 177 CYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7839 (m) REVERT: F 178 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8237 (mmmt) REVERT: F 191 ASP cc_start: 0.8457 (p0) cc_final: 0.7814 (p0) REVERT: F 192 LYS cc_start: 0.8702 (mmtt) cc_final: 0.7957 (mmtt) REVERT: F 193 GLN cc_start: 0.8654 (mm110) cc_final: 0.8317 (mm110) REVERT: F 194 LEU cc_start: 0.8773 (mt) cc_final: 0.8487 (mm) REVERT: F 198 GLN cc_start: 0.8333 (pm20) cc_final: 0.7748 (tp40) REVERT: F 215 PHE cc_start: 0.6697 (m-80) cc_final: 0.6392 (m-80) REVERT: F 253 LEU cc_start: 0.9064 (mm) cc_final: 0.8786 (mt) REVERT: F 271 ASN cc_start: 0.8435 (p0) cc_final: 0.8183 (p0) REVERT: F 277 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7768 (mtt) REVERT: F 284 LEU cc_start: 0.6803 (mt) cc_final: 0.6123 (tt) REVERT: F 313 GLN cc_start: 0.8844 (mp10) cc_final: 0.8431 (pt0) REVERT: F 325 ASP cc_start: 0.8065 (m-30) cc_final: 0.7699 (m-30) REVERT: F 327 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7898 (mm-30) REVERT: F 330 ARG cc_start: 0.8197 (ptt90) cc_final: 0.7993 (ptt90) REVERT: F 333 MET cc_start: 0.7846 (tpp) cc_final: 0.7481 (mpp) REVERT: F 334 MET cc_start: 0.8169 (tpt) cc_final: 0.7807 (tpt) REVERT: F 346 MET cc_start: 0.7685 (mtt) cc_final: 0.6858 (mtt) REVERT: F 349 PHE cc_start: 0.8696 (t80) cc_final: 0.7873 (t80) REVERT: F 355 MET cc_start: 0.8161 (tpp) cc_final: 0.7251 (tpp) REVERT: F 356 GLN cc_start: 0.8527 (tt0) cc_final: 0.7951 (tm-30) REVERT: F 357 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8007 (ttt-90) REVERT: F 358 LYS cc_start: 0.8660 (mtpp) cc_final: 0.7892 (mtpp) REVERT: F 362 THR cc_start: 0.8779 (t) cc_final: 0.8450 (p) REVERT: F 368 ARG cc_start: 0.7737 (ttt-90) cc_final: 0.6498 (ttm110) REVERT: F 369 GLN cc_start: 0.6835 (tm-30) cc_final: 0.5939 (tm-30) REVERT: F 373 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7760 (ttp80) REVERT: F 394 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6892 (t-90) REVERT: F 405 SER cc_start: 0.8677 (t) cc_final: 0.8462 (p) REVERT: F 419 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8383 (p) REVERT: F 423 PHE cc_start: 0.8572 (t80) cc_final: 0.8244 (t80) REVERT: F 434 VAL cc_start: 0.8336 (p) cc_final: 0.8068 (m) REVERT: F 435 TRP cc_start: 0.8090 (t60) cc_final: 0.7878 (t60) REVERT: F 437 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (mm110) REVERT: F 448 GLN cc_start: 0.8824 (mt0) cc_final: 0.8257 (mt0) REVERT: F 464 GLU cc_start: 0.7978 (tp30) cc_final: 0.7594 (tp30) REVERT: F 482 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8177 (mmtp) REVERT: F 484 LEU cc_start: 0.8583 (mt) cc_final: 0.8321 (mt) REVERT: F 485 GLN cc_start: 0.7647 (mt0) cc_final: 0.7392 (mt0) REVERT: F 495 SER cc_start: 0.7982 (t) cc_final: 0.7162 (p) REVERT: F 498 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7847 (tp-100) REVERT: F 499 ASN cc_start: 0.8284 (m-40) cc_final: 0.7832 (m110) REVERT: F 501 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8175 (ttm110) REVERT: F 502 ASN cc_start: 0.7853 (t0) cc_final: 0.7345 (t0) REVERT: F 503 PHE cc_start: 0.8589 (t80) cc_final: 0.8356 (t80) REVERT: F 505 LEU cc_start: 0.8613 (mm) cc_final: 0.8390 (mm) REVERT: F 528 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.4832 (ttp-170) REVERT: F 539 TYR cc_start: 0.8169 (t80) cc_final: 0.7466 (t80) REVERT: F 575 HIS cc_start: 0.8741 (m90) cc_final: 0.8167 (m90) REVERT: F 576 ARG cc_start: 0.7520 (mmp80) cc_final: 0.6972 (mtm-85) REVERT: F 581 ASN cc_start: 0.8306 (t0) cc_final: 0.7900 (t0) REVERT: F 583 GLN cc_start: 0.8781 (mm110) cc_final: 0.8543 (mm110) REVERT: F 587 GLU cc_start: 0.8162 (tt0) cc_final: 0.7806 (tt0) REVERT: F 611 LYS cc_start: 0.8568 (pttt) cc_final: 0.8163 (mmtm) REVERT: F 616 LEU cc_start: 0.8209 (tt) cc_final: 0.7953 (mm) REVERT: F 617 TRP cc_start: 0.8305 (t60) cc_final: 0.7918 (t60) REVERT: F 621 TYR cc_start: 0.8575 (t80) cc_final: 0.8112 (t80) REVERT: F 623 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7586 (ttp80) REVERT: F 628 GLU cc_start: 0.8294 (pt0) cc_final: 0.7511 (pt0) REVERT: F 637 PHE cc_start: 0.8308 (m-80) cc_final: 0.8091 (m-80) REVERT: F 646 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7936 (t0) REVERT: F 672 GLU cc_start: 0.8267 (pp20) cc_final: 0.7783 (pp20) REVERT: F 676 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7781 (ttm-80) REVERT: F 684 ASP cc_start: 0.8271 (t0) cc_final: 0.8050 (t0) outliers start: 55 outliers final: 30 residues processed: 400 average time/residue: 0.3478 time to fit residues: 175.9946 Evaluate side-chains 423 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 377 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 CYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 419 CYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 664 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 HIS ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100247 restraints weight = 15020.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104008 restraints weight = 7707.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106543 restraints weight = 4728.495| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6998 Z= 0.124 Angle : 0.734 12.852 9480 Z= 0.357 Chirality : 0.044 0.150 1059 Planarity : 0.004 0.047 1227 Dihedral : 4.698 55.314 936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.28 % Allowed : 31.78 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 835 helix: 1.49 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 535 HIS 0.005 0.001 HIS F 633 PHE 0.023 0.001 PHE G 503 TYR 0.027 0.001 TYR F 546 ARG 0.011 0.001 ARG F 316 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 342) hydrogen bonds : angle 4.43384 ( 984) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.71268 ( 4) covalent geometry : bond 0.00278 ( 6996) covalent geometry : angle 0.73408 ( 9476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 387 time to evaluate : 1.912 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 182 SER cc_start: 0.8357 (p) cc_final: 0.7660 (t) REVERT: G 192 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8637 (mtmt) REVERT: G 201 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8051 (m) REVERT: G 204 ASP cc_start: 0.7606 (t70) cc_final: 0.7200 (t0) REVERT: G 223 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7900 (mtmm) REVERT: G 258 ARG cc_start: 0.6892 (mtt180) cc_final: 0.6553 (mtt180) REVERT: G 272 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8583 (mm) REVERT: G 277 MET cc_start: 0.8116 (mmm) cc_final: 0.7638 (mmm) REVERT: G 288 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7257 (tpt170) REVERT: G 290 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7588 (mtp85) REVERT: G 293 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7030 (tm-30) REVERT: G 294 ARG cc_start: 0.5697 (tmt-80) cc_final: 0.4486 (tmt170) REVERT: G 312 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 314 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8257 (pp) REVERT: G 318 LEU cc_start: 0.8883 (tp) cc_final: 0.8507 (tp) REVERT: G 327 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8032 (tm-30) REVERT: G 342 GLU cc_start: 0.7880 (mp0) cc_final: 0.7346 (mp0) REVERT: G 344 GLU cc_start: 0.8197 (tp30) cc_final: 0.6561 (tp30) REVERT: G 347 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8007 (tm-30) REVERT: G 349 PHE cc_start: 0.8907 (t80) cc_final: 0.8566 (t80) REVERT: G 355 MET cc_start: 0.7971 (tpp) cc_final: 0.6984 (tpp) REVERT: G 359 LEU cc_start: 0.8988 (mt) cc_final: 0.8442 (mm) REVERT: G 412 ARG cc_start: 0.8537 (ttt180) cc_final: 0.7912 (ttt-90) REVERT: G 417 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8370 (mtm-85) REVERT: G 419 CYS cc_start: 0.8624 (m) cc_final: 0.8044 (m) REVERT: G 423 PHE cc_start: 0.8600 (t80) cc_final: 0.8310 (t80) REVERT: G 425 CYS cc_start: 0.8831 (m) cc_final: 0.8471 (m) REVERT: G 426 TYR cc_start: 0.8579 (t80) cc_final: 0.8333 (t80) REVERT: G 429 GLN cc_start: 0.8387 (tt0) cc_final: 0.8020 (tt0) REVERT: G 432 MET cc_start: 0.7939 (mmm) cc_final: 0.7574 (mmm) REVERT: G 443 ASN cc_start: 0.8268 (m-40) cc_final: 0.7603 (m-40) REVERT: G 445 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8400 (mptp) REVERT: G 446 GLU cc_start: 0.7737 (tt0) cc_final: 0.7161 (pt0) REVERT: G 448 GLN cc_start: 0.8396 (mt0) cc_final: 0.7325 (mt0) REVERT: G 449 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7582 (mmmm) REVERT: G 452 LYS cc_start: 0.8590 (mttm) cc_final: 0.7875 (mttm) REVERT: G 453 GLN cc_start: 0.8242 (mt0) cc_final: 0.7715 (mp10) REVERT: G 456 LYS cc_start: 0.9237 (tmtm) cc_final: 0.8800 (tmtm) REVERT: G 458 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7939 (mm) REVERT: G 478 GLU cc_start: 0.8478 (pm20) cc_final: 0.8132 (pm20) REVERT: G 482 LYS cc_start: 0.8484 (tptp) cc_final: 0.7812 (tptp) REVERT: G 495 SER cc_start: 0.8744 (m) cc_final: 0.8248 (p) REVERT: G 497 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (mm) REVERT: G 498 GLN cc_start: 0.8635 (tp40) cc_final: 0.7711 (tp40) REVERT: G 501 ARG cc_start: 0.8667 (ttp-170) cc_final: 0.7970 (ptp-110) REVERT: G 502 ASN cc_start: 0.8160 (t0) cc_final: 0.7180 (t0) REVERT: G 504 ILE cc_start: 0.8669 (mm) cc_final: 0.8392 (mm) REVERT: G 506 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7466 (mm-30) REVERT: G 507 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8084 (mmm160) REVERT: G 522 PHE cc_start: 0.8525 (m-80) cc_final: 0.8313 (m-10) REVERT: G 540 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8499 (mm) REVERT: F 167 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5870 (pt) REVERT: F 173 PHE cc_start: 0.7922 (m-80) cc_final: 0.7610 (m-80) REVERT: F 175 GLN cc_start: 0.7382 (tm130) cc_final: 0.7082 (tm-30) REVERT: F 176 ASN cc_start: 0.8277 (t0) cc_final: 0.7958 (m110) REVERT: F 177 CYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7829 (m) REVERT: F 178 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8242 (mmmt) REVERT: F 191 ASP cc_start: 0.8430 (p0) cc_final: 0.7813 (p0) REVERT: F 192 LYS cc_start: 0.8687 (mmtt) cc_final: 0.7944 (mmtt) REVERT: F 193 GLN cc_start: 0.8663 (mm110) cc_final: 0.8324 (mm110) REVERT: F 194 LEU cc_start: 0.8757 (mt) cc_final: 0.8455 (mm) REVERT: F 198 GLN cc_start: 0.8316 (pm20) cc_final: 0.7646 (tp40) REVERT: F 215 PHE cc_start: 0.6713 (m-80) cc_final: 0.6398 (m-80) REVERT: F 253 LEU cc_start: 0.9049 (mm) cc_final: 0.8782 (mt) REVERT: F 271 ASN cc_start: 0.8408 (p0) cc_final: 0.8066 (p0) REVERT: F 277 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7857 (mtt) REVERT: F 284 LEU cc_start: 0.6868 (mt) cc_final: 0.6199 (tt) REVERT: F 313 GLN cc_start: 0.8640 (mp10) cc_final: 0.8027 (pt0) REVERT: F 322 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7083 (pm20) REVERT: F 325 ASP cc_start: 0.8056 (m-30) cc_final: 0.7484 (m-30) REVERT: F 327 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7938 (mm-30) REVERT: F 330 ARG cc_start: 0.8174 (ptt90) cc_final: 0.7956 (ptt90) REVERT: F 333 MET cc_start: 0.7827 (tpp) cc_final: 0.7523 (mpp) REVERT: F 334 MET cc_start: 0.8231 (tpt) cc_final: 0.7858 (tpt) REVERT: F 342 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7507 (mm-30) REVERT: F 346 MET cc_start: 0.7659 (mtt) cc_final: 0.6974 (mtt) REVERT: F 349 PHE cc_start: 0.8712 (t80) cc_final: 0.7877 (t80) REVERT: F 355 MET cc_start: 0.8160 (tpp) cc_final: 0.7242 (tpp) REVERT: F 356 GLN cc_start: 0.8550 (tt0) cc_final: 0.7989 (tm-30) REVERT: F 357 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7997 (ttt-90) REVERT: F 358 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8099 (mtpp) REVERT: F 368 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7520 (ttm-80) REVERT: F 369 GLN cc_start: 0.6887 (tm-30) cc_final: 0.5994 (tm-30) REVERT: F 373 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7751 (ttp80) REVERT: F 394 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: F 419 CYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8371 (p) REVERT: F 427 THR cc_start: 0.8823 (p) cc_final: 0.8529 (t) REVERT: F 437 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: F 448 GLN cc_start: 0.8782 (mt0) cc_final: 0.8233 (mt0) REVERT: F 464 GLU cc_start: 0.8034 (tp30) cc_final: 0.7570 (tp30) REVERT: F 482 LYS cc_start: 0.8429 (mmtp) cc_final: 0.8166 (mmtp) REVERT: F 484 LEU cc_start: 0.8570 (mt) cc_final: 0.8330 (mt) REVERT: F 485 GLN cc_start: 0.7673 (mt0) cc_final: 0.7432 (mt0) REVERT: F 495 SER cc_start: 0.7963 (t) cc_final: 0.7124 (p) REVERT: F 498 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7868 (tp-100) REVERT: F 499 ASN cc_start: 0.8308 (m-40) cc_final: 0.7816 (m110) REVERT: F 501 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8118 (ttm110) REVERT: F 502 ASN cc_start: 0.7868 (t0) cc_final: 0.7352 (t0) REVERT: F 503 PHE cc_start: 0.8565 (t80) cc_final: 0.8346 (t80) REVERT: F 505 LEU cc_start: 0.8645 (mm) cc_final: 0.8423 (mm) REVERT: F 528 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.5623 (mtm180) REVERT: F 539 TYR cc_start: 0.8120 (t80) cc_final: 0.7565 (t80) REVERT: F 575 HIS cc_start: 0.8712 (m90) cc_final: 0.8154 (m90) REVERT: F 576 ARG cc_start: 0.7500 (mmp80) cc_final: 0.6963 (mtm-85) REVERT: F 581 ASN cc_start: 0.8281 (t0) cc_final: 0.7854 (t0) REVERT: F 583 GLN cc_start: 0.8765 (mm110) cc_final: 0.8536 (mm110) REVERT: F 587 GLU cc_start: 0.8161 (tt0) cc_final: 0.7847 (tt0) REVERT: F 611 LYS cc_start: 0.8499 (pttt) cc_final: 0.8064 (mmtm) REVERT: F 616 LEU cc_start: 0.8189 (tt) cc_final: 0.7957 (mm) REVERT: F 617 TRP cc_start: 0.8211 (t60) cc_final: 0.7820 (t60) REVERT: F 621 TYR cc_start: 0.8537 (t80) cc_final: 0.8133 (t80) REVERT: F 623 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7610 (ttp80) REVERT: F 628 GLU cc_start: 0.8295 (pt0) cc_final: 0.7527 (pt0) REVERT: F 646 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7914 (t0) REVERT: F 672 GLU cc_start: 0.8256 (pp20) cc_final: 0.7763 (pp20) REVERT: F 676 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: F 684 ASP cc_start: 0.8254 (t0) cc_final: 0.8048 (t0) outliers start: 47 outliers final: 24 residues processed: 403 average time/residue: 0.3034 time to fit residues: 154.9046 Evaluate side-chains 422 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 CYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 419 CYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 597 GLN Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 HIS ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099126 restraints weight = 15156.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102880 restraints weight = 7755.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105440 restraints weight = 4760.887| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6998 Z= 0.145 Angle : 0.750 12.585 9480 Z= 0.367 Chirality : 0.045 0.158 1059 Planarity : 0.004 0.037 1227 Dihedral : 4.721 54.563 936 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.01 % Allowed : 32.98 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 835 helix: 1.51 (0.25), residues: 473 sheet: -0.55 (1.91), residues: 12 loop : -1.22 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 535 HIS 0.013 0.001 HIS F 264 PHE 0.026 0.001 PHE F 423 TYR 0.028 0.001 TYR F 546 ARG 0.008 0.001 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 342) hydrogen bonds : angle 4.44860 ( 984) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.54597 ( 4) covalent geometry : bond 0.00318 ( 6996) covalent geometry : angle 0.74970 ( 9476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 391 time to evaluate : 0.748 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: G 182 SER cc_start: 0.8351 (p) cc_final: 0.7660 (t) REVERT: G 192 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8561 (mtmt) REVERT: G 201 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8064 (m) REVERT: G 204 ASP cc_start: 0.7620 (t70) cc_final: 0.7212 (t0) REVERT: G 223 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7924 (mtmm) REVERT: G 257 LYS cc_start: 0.8868 (mttt) cc_final: 0.8618 (mttt) REVERT: G 258 ARG cc_start: 0.6907 (mtt180) cc_final: 0.6541 (mtt180) REVERT: G 272 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8607 (mm) REVERT: G 277 MET cc_start: 0.8143 (mmm) cc_final: 0.7684 (mmm) REVERT: G 283 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6715 (mm-30) REVERT: G 288 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7244 (tpt170) REVERT: G 290 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7586 (mtp85) REVERT: G 293 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7032 (tm-30) REVERT: G 294 ARG cc_start: 0.5802 (tmt-80) cc_final: 0.4643 (tmt170) REVERT: G 312 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7716 (tm-30) REVERT: G 314 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8286 (pp) REVERT: G 318 LEU cc_start: 0.8879 (tp) cc_final: 0.8523 (tp) REVERT: G 327 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8035 (tm-30) REVERT: G 338 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7963 (mp) REVERT: G 342 GLU cc_start: 0.7930 (mp0) cc_final: 0.7381 (mp0) REVERT: G 344 GLU cc_start: 0.8205 (tp30) cc_final: 0.6634 (tp30) REVERT: G 347 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8222 (tm-30) REVERT: G 349 PHE cc_start: 0.8917 (t80) cc_final: 0.8588 (t80) REVERT: G 355 MET cc_start: 0.8018 (tpp) cc_final: 0.7001 (tpp) REVERT: G 359 LEU cc_start: 0.8965 (mt) cc_final: 0.8466 (mm) REVERT: G 412 ARG cc_start: 0.8521 (ttt180) cc_final: 0.7888 (ttt-90) REVERT: G 417 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: G 419 CYS cc_start: 0.8581 (m) cc_final: 0.8038 (m) REVERT: G 423 PHE cc_start: 0.8650 (t80) cc_final: 0.8260 (t80) REVERT: G 425 CYS cc_start: 0.8806 (m) cc_final: 0.8423 (m) REVERT: G 426 TYR cc_start: 0.8586 (t80) cc_final: 0.8333 (t80) REVERT: G 429 GLN cc_start: 0.8404 (tt0) cc_final: 0.8023 (tt0) REVERT: G 432 MET cc_start: 0.7850 (mmm) cc_final: 0.7544 (mmm) REVERT: G 437 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 445 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8386 (mptp) REVERT: G 448 GLN cc_start: 0.8451 (mt0) cc_final: 0.7564 (mt0) REVERT: G 449 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7572 (mmmm) REVERT: G 452 LYS cc_start: 0.8613 (mttm) cc_final: 0.8035 (mttm) REVERT: G 453 GLN cc_start: 0.8274 (mt0) cc_final: 0.7759 (mp10) REVERT: G 456 LYS cc_start: 0.9229 (tmtm) cc_final: 0.8791 (tmtm) REVERT: G 458 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7961 (mm) REVERT: G 478 GLU cc_start: 0.8514 (pm20) cc_final: 0.8168 (pm20) REVERT: G 482 LYS cc_start: 0.8506 (tptp) cc_final: 0.7890 (tptp) REVERT: G 495 SER cc_start: 0.8743 (m) cc_final: 0.8230 (p) REVERT: G 497 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8566 (mm) REVERT: G 498 GLN cc_start: 0.8633 (tp40) cc_final: 0.7633 (tp40) REVERT: G 501 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.7937 (ptp-110) REVERT: G 502 ASN cc_start: 0.8178 (t0) cc_final: 0.7233 (t0) REVERT: G 504 ILE cc_start: 0.8678 (mm) cc_final: 0.8406 (mm) REVERT: G 506 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7592 (mm-30) REVERT: G 507 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8070 (mmm160) REVERT: G 518 LEU cc_start: 0.8053 (mt) cc_final: 0.7737 (mt) REVERT: G 526 LYS cc_start: 0.7923 (pttt) cc_final: 0.7718 (pttt) REVERT: G 540 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8537 (mm) REVERT: F 167 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5949 (pt) REVERT: F 173 PHE cc_start: 0.7926 (m-80) cc_final: 0.7608 (m-80) REVERT: F 175 GLN cc_start: 0.7422 (tm130) cc_final: 0.7070 (tm-30) REVERT: F 176 ASN cc_start: 0.8278 (t0) cc_final: 0.7985 (m110) REVERT: F 177 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7749 (m) REVERT: F 178 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8212 (mmmt) REVERT: F 191 ASP cc_start: 0.8423 (p0) cc_final: 0.7817 (p0) REVERT: F 192 LYS cc_start: 0.8685 (mmtt) cc_final: 0.7936 (mmtt) REVERT: F 193 GLN cc_start: 0.8665 (mm110) cc_final: 0.8332 (mm110) REVERT: F 194 LEU cc_start: 0.8737 (mt) cc_final: 0.8448 (mm) REVERT: F 198 GLN cc_start: 0.8340 (pm20) cc_final: 0.7735 (tp40) REVERT: F 215 PHE cc_start: 0.6718 (m-80) cc_final: 0.6415 (m-80) REVERT: F 271 ASN cc_start: 0.8488 (p0) cc_final: 0.8213 (p0) REVERT: F 277 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7926 (mtt) REVERT: F 284 LEU cc_start: 0.6889 (mt) cc_final: 0.6240 (tt) REVERT: F 322 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7058 (mt-10) REVERT: F 325 ASP cc_start: 0.8051 (m-30) cc_final: 0.7577 (m-30) REVERT: F 327 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8174 (mm-30) REVERT: F 330 ARG cc_start: 0.8191 (ptt90) cc_final: 0.7897 (ptt90) REVERT: F 333 MET cc_start: 0.7906 (tpp) cc_final: 0.7613 (mpp) REVERT: F 334 MET cc_start: 0.8258 (tpt) cc_final: 0.7874 (tpt) REVERT: F 346 MET cc_start: 0.7666 (mtt) cc_final: 0.6966 (mtt) REVERT: F 349 PHE cc_start: 0.8716 (t80) cc_final: 0.7898 (t80) REVERT: F 355 MET cc_start: 0.8152 (tpp) cc_final: 0.7245 (tpp) REVERT: F 356 GLN cc_start: 0.8549 (tt0) cc_final: 0.8007 (tm-30) REVERT: F 357 ARG cc_start: 0.8492 (ttt180) cc_final: 0.8025 (ttt-90) REVERT: F 358 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8116 (mtpp) REVERT: F 360 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8272 (mt-10) REVERT: F 368 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7462 (ttt-90) REVERT: F 369 GLN cc_start: 0.6895 (tm-30) cc_final: 0.5995 (tm-30) REVERT: F 373 ARG cc_start: 0.8250 (ttt180) cc_final: 0.7765 (ttp80) REVERT: F 382 GLU cc_start: 0.8201 (tp30) cc_final: 0.7964 (tp30) REVERT: F 394 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: F 419 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8386 (p) REVERT: F 427 THR cc_start: 0.8861 (p) cc_final: 0.8562 (t) REVERT: F 437 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7744 (mm110) REVERT: F 448 GLN cc_start: 0.8787 (mt0) cc_final: 0.8273 (mt0) REVERT: F 464 GLU cc_start: 0.8053 (tp30) cc_final: 0.7555 (tp30) REVERT: F 484 LEU cc_start: 0.8486 (mt) cc_final: 0.8239 (mt) REVERT: F 495 SER cc_start: 0.8004 (t) cc_final: 0.7152 (p) REVERT: F 498 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8122 (tp40) REVERT: F 499 ASN cc_start: 0.8281 (m-40) cc_final: 0.7793 (m110) REVERT: F 501 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8084 (ttm110) REVERT: F 502 ASN cc_start: 0.7845 (t0) cc_final: 0.7355 (t0) REVERT: F 503 PHE cc_start: 0.8570 (t80) cc_final: 0.8341 (t80) REVERT: F 505 LEU cc_start: 0.8719 (mm) cc_final: 0.8478 (mm) REVERT: F 528 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.5616 (mtm180) REVERT: F 539 TYR cc_start: 0.8146 (t80) cc_final: 0.7503 (t80) REVERT: F 575 HIS cc_start: 0.8712 (m90) cc_final: 0.8166 (m90) REVERT: F 576 ARG cc_start: 0.7541 (mmp80) cc_final: 0.7006 (mtm-85) REVERT: F 581 ASN cc_start: 0.8290 (t0) cc_final: 0.7869 (t0) REVERT: F 583 GLN cc_start: 0.8770 (mm110) cc_final: 0.8542 (mm110) REVERT: F 587 GLU cc_start: 0.8264 (tt0) cc_final: 0.7939 (tt0) REVERT: F 611 LYS cc_start: 0.8520 (pttt) cc_final: 0.8119 (mmtm) REVERT: F 616 LEU cc_start: 0.8186 (tt) cc_final: 0.7957 (mm) REVERT: F 617 TRP cc_start: 0.8186 (t60) cc_final: 0.7786 (t60) REVERT: F 621 TYR cc_start: 0.8549 (t80) cc_final: 0.8122 (t80) REVERT: F 623 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7637 (ttp80) REVERT: F 628 GLU cc_start: 0.8283 (pt0) cc_final: 0.7526 (pt0) REVERT: F 646 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7924 (t0) REVERT: F 676 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: F 684 ASP cc_start: 0.8227 (t0) cc_final: 0.8004 (t0) outliers start: 45 outliers final: 26 residues processed: 405 average time/residue: 0.2246 time to fit residues: 114.2626 Evaluate side-chains 427 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 459 TRP Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 CYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 419 CYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 597 GLN Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 664 GLN Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 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 = 0.3754 r_free = 0.3754 target = 0.118332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099518 restraints weight = 15172.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.103320 restraints weight = 7750.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105855 restraints weight = 4749.948| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6998 Z= 0.135 Angle : 0.770 12.165 9480 Z= 0.377 Chirality : 0.045 0.166 1059 Planarity : 0.004 0.039 1227 Dihedral : 4.737 54.434 936 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.01 % Allowed : 33.38 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.30), residues: 835 helix: 1.46 (0.25), residues: 473 sheet: -0.62 (1.90), residues: 12 loop : -1.22 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 435 HIS 0.011 0.001 HIS F 264 PHE 0.024 0.001 PHE F 423 TYR 0.029 0.001 TYR F 546 ARG 0.015 0.001 ARG F 316 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 342) hydrogen bonds : angle 4.41705 ( 984) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.64211 ( 4) covalent geometry : bond 0.00307 ( 6996) covalent geometry : angle 0.77005 ( 9476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 386 time to evaluate : 0.734 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: G 174 PHE cc_start: 0.7141 (m-10) cc_final: 0.6893 (m-10) REVERT: G 182 SER cc_start: 0.8330 (p) cc_final: 0.7637 (t) REVERT: G 192 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8588 (mtmt) REVERT: G 201 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8037 (m) REVERT: G 204 ASP cc_start: 0.7611 (t70) cc_final: 0.7197 (t0) REVERT: G 223 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7918 (mtmm) REVERT: G 257 LYS cc_start: 0.8911 (mttt) cc_final: 0.8596 (mttt) REVERT: G 258 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6524 (mtt180) REVERT: G 272 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8588 (mm) REVERT: G 277 MET cc_start: 0.8168 (mmm) cc_final: 0.7655 (mmm) REVERT: G 283 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6703 (mm-30) REVERT: G 288 ARG cc_start: 0.8090 (tpp-160) cc_final: 0.7249 (tpt170) REVERT: G 290 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7582 (mtp85) REVERT: G 293 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6960 (tm-30) REVERT: G 294 ARG cc_start: 0.5876 (tmt-80) cc_final: 0.4733 (tmt170) REVERT: G 312 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7691 (tm-30) REVERT: G 314 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8323 (pp) REVERT: G 318 LEU cc_start: 0.8890 (tp) cc_final: 0.8648 (tp) REVERT: G 327 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8053 (tm-30) REVERT: G 338 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7966 (mp) REVERT: G 342 GLU cc_start: 0.7934 (mp0) cc_final: 0.7390 (mp0) REVERT: G 344 GLU cc_start: 0.8199 (tp30) cc_final: 0.6646 (tp30) REVERT: G 347 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8203 (tm-30) REVERT: G 349 PHE cc_start: 0.8901 (t80) cc_final: 0.8436 (t80) REVERT: G 350 PHE cc_start: 0.9028 (m-10) cc_final: 0.8782 (m-80) REVERT: G 355 MET cc_start: 0.8022 (tpp) cc_final: 0.6993 (tpp) REVERT: G 359 LEU cc_start: 0.8964 (mt) cc_final: 0.8504 (mm) REVERT: G 412 ARG cc_start: 0.8516 (ttt180) cc_final: 0.7875 (ttt-90) REVERT: G 417 ARG cc_start: 0.8744 (mtm110) cc_final: 0.8391 (mtm-85) REVERT: G 419 CYS cc_start: 0.8578 (m) cc_final: 0.8034 (m) REVERT: G 423 PHE cc_start: 0.8635 (t80) cc_final: 0.8239 (t80) REVERT: G 425 CYS cc_start: 0.8793 (m) cc_final: 0.8395 (m) REVERT: G 426 TYR cc_start: 0.8608 (t80) cc_final: 0.8386 (t80) REVERT: G 429 GLN cc_start: 0.8411 (tt0) cc_final: 0.8046 (tt0) REVERT: G 432 MET cc_start: 0.7869 (mmm) cc_final: 0.7555 (mmm) REVERT: G 437 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8077 (tm-30) REVERT: G 445 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8442 (mptp) REVERT: G 448 GLN cc_start: 0.8423 (mt0) cc_final: 0.7582 (mt0) REVERT: G 449 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7570 (mmmm) REVERT: G 452 LYS cc_start: 0.8625 (mttm) cc_final: 0.8031 (mttm) REVERT: G 453 GLN cc_start: 0.8263 (mt0) cc_final: 0.7772 (mp10) REVERT: G 456 LYS cc_start: 0.9248 (tmtm) cc_final: 0.8786 (tmtm) REVERT: G 458 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7968 (mm) REVERT: G 478 GLU cc_start: 0.8518 (pm20) cc_final: 0.8176 (pm20) REVERT: G 482 LYS cc_start: 0.8485 (tptp) cc_final: 0.7817 (tptp) REVERT: G 495 SER cc_start: 0.8741 (m) cc_final: 0.8234 (p) REVERT: G 497 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8569 (mm) REVERT: G 498 GLN cc_start: 0.8632 (tp40) cc_final: 0.7623 (tp40) REVERT: G 501 ARG cc_start: 0.8663 (ttp-170) cc_final: 0.7930 (ptp-110) REVERT: G 502 ASN cc_start: 0.8164 (t0) cc_final: 0.7228 (t0) REVERT: G 504 ILE cc_start: 0.8684 (mm) cc_final: 0.8322 (mm) REVERT: G 506 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7551 (mm-30) REVERT: G 507 ARG cc_start: 0.8329 (mmm-85) cc_final: 0.8061 (mmm160) REVERT: G 518 LEU cc_start: 0.8096 (mt) cc_final: 0.7723 (mt) REVERT: G 540 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8464 (mm) REVERT: F 167 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5933 (pt) REVERT: F 173 PHE cc_start: 0.7913 (m-80) cc_final: 0.7599 (m-80) REVERT: F 175 GLN cc_start: 0.7422 (tm130) cc_final: 0.7081 (tm-30) REVERT: F 176 ASN cc_start: 0.8258 (t0) cc_final: 0.7979 (m110) REVERT: F 177 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7676 (m) REVERT: F 178 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8207 (mmmt) REVERT: F 191 ASP cc_start: 0.8425 (p0) cc_final: 0.8155 (p0) REVERT: F 192 LYS cc_start: 0.8675 (mmtt) cc_final: 0.7996 (mmtt) REVERT: F 193 GLN cc_start: 0.8674 (mm110) cc_final: 0.8418 (mm110) REVERT: F 194 LEU cc_start: 0.8730 (mt) cc_final: 0.8454 (mm) REVERT: F 197 ARG cc_start: 0.7631 (ptp-170) cc_final: 0.7291 (ptp-110) REVERT: F 198 GLN cc_start: 0.8319 (pm20) cc_final: 0.7729 (tp40) REVERT: F 215 PHE cc_start: 0.6707 (m-80) cc_final: 0.6412 (m-80) REVERT: F 253 LEU cc_start: 0.9043 (mm) cc_final: 0.8786 (mt) REVERT: F 271 ASN cc_start: 0.8519 (p0) cc_final: 0.8235 (p0) REVERT: F 277 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7894 (mtt) REVERT: F 284 LEU cc_start: 0.6963 (mt) cc_final: 0.6294 (tt) REVERT: F 322 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7114 (mt-10) REVERT: F 325 ASP cc_start: 0.8026 (m-30) cc_final: 0.7571 (m-30) REVERT: F 334 MET cc_start: 0.8241 (tpt) cc_final: 0.7853 (tpt) REVERT: F 346 MET cc_start: 0.7693 (mtt) cc_final: 0.6968 (mtt) REVERT: F 347 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7756 (tp40) REVERT: F 349 PHE cc_start: 0.8724 (t80) cc_final: 0.7892 (t80) REVERT: F 355 MET cc_start: 0.8149 (tpp) cc_final: 0.7248 (tpp) REVERT: F 356 GLN cc_start: 0.8574 (tt0) cc_final: 0.8113 (tm-30) REVERT: F 357 ARG cc_start: 0.8484 (ttt180) cc_final: 0.8013 (ttt-90) REVERT: F 358 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8111 (mtpp) REVERT: F 360 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8320 (mt-10) REVERT: F 369 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6011 (tm-30) REVERT: F 373 ARG cc_start: 0.8223 (ttt180) cc_final: 0.7774 (ttp80) REVERT: F 394 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.6971 (t-90) REVERT: F 419 CYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8384 (p) REVERT: F 427 THR cc_start: 0.8863 (p) cc_final: 0.8566 (t) REVERT: F 434 VAL cc_start: 0.8343 (p) cc_final: 0.8077 (m) REVERT: F 437 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7751 (mm110) REVERT: F 446 GLU cc_start: 0.8382 (tt0) cc_final: 0.8141 (tt0) REVERT: F 448 GLN cc_start: 0.8775 (mt0) cc_final: 0.8251 (mt0) REVERT: F 464 GLU cc_start: 0.8056 (tp30) cc_final: 0.7547 (tp30) REVERT: F 484 LEU cc_start: 0.8494 (mt) cc_final: 0.8252 (mt) REVERT: F 494 GLN cc_start: 0.8440 (mt0) cc_final: 0.8032 (mt0) REVERT: F 495 SER cc_start: 0.8002 (t) cc_final: 0.7125 (p) REVERT: F 498 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8102 (tp40) REVERT: F 499 ASN cc_start: 0.8252 (m-40) cc_final: 0.7835 (m110) REVERT: F 501 ARG cc_start: 0.8487 (ttm110) cc_final: 0.8084 (ttm110) REVERT: F 502 ASN cc_start: 0.7832 (t0) cc_final: 0.7339 (t0) REVERT: F 503 PHE cc_start: 0.8560 (t80) cc_final: 0.8337 (t80) REVERT: F 505 LEU cc_start: 0.8721 (mm) cc_final: 0.8489 (mm) REVERT: F 528 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.5721 (mtm180) REVERT: F 534 LEU cc_start: 0.8658 (mt) cc_final: 0.8427 (mm) REVERT: F 539 TYR cc_start: 0.8176 (t80) cc_final: 0.7432 (t80) REVERT: F 541 LEU cc_start: 0.8674 (tp) cc_final: 0.8416 (tt) REVERT: F 575 HIS cc_start: 0.8678 (m90) cc_final: 0.8162 (m90) REVERT: F 576 ARG cc_start: 0.7535 (mmp80) cc_final: 0.7032 (mtm-85) REVERT: F 581 ASN cc_start: 0.8272 (t0) cc_final: 0.7831 (t0) REVERT: F 583 GLN cc_start: 0.8768 (mm110) cc_final: 0.8548 (mm110) REVERT: F 587 GLU cc_start: 0.8261 (tt0) cc_final: 0.7921 (tt0) REVERT: F 611 LYS cc_start: 0.8534 (pttt) cc_final: 0.8085 (mmtp) REVERT: F 616 LEU cc_start: 0.8183 (tt) cc_final: 0.7955 (mm) REVERT: F 617 TRP cc_start: 0.8226 (t60) cc_final: 0.7832 (t60) REVERT: F 621 TYR cc_start: 0.8552 (t80) cc_final: 0.8151 (t80) REVERT: F 623 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7650 (ttp80) REVERT: F 628 GLU cc_start: 0.8280 (pt0) cc_final: 0.7531 (pt0) REVERT: F 646 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (t0) REVERT: F 672 GLU cc_start: 0.8209 (pp20) cc_final: 0.7802 (pp20) REVERT: F 676 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7814 (ttm-80) outliers start: 45 outliers final: 25 residues processed: 401 average time/residue: 0.2279 time to fit residues: 115.3479 Evaluate side-chains 421 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 459 TRP Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 CYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 419 CYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 664 GLN Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS F 313 GLN F 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097815 restraints weight = 15479.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101622 restraints weight = 7865.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104133 restraints weight = 4805.033| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6998 Z= 0.159 Angle : 0.791 12.074 9480 Z= 0.392 Chirality : 0.046 0.175 1059 Planarity : 0.005 0.039 1227 Dihedral : 4.773 51.500 936 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.74 % Allowed : 34.45 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 835 helix: 1.36 (0.24), residues: 474 sheet: -0.67 (1.84), residues: 12 loop : -1.24 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 459 HIS 0.008 0.001 HIS F 264 PHE 0.024 0.001 PHE F 423 TYR 0.030 0.001 TYR F 546 ARG 0.008 0.000 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 342) hydrogen bonds : angle 4.50314 ( 984) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.52164 ( 4) covalent geometry : bond 0.00343 ( 6996) covalent geometry : angle 0.79119 ( 9476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 0.976 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: G 174 PHE cc_start: 0.7194 (m-10) cc_final: 0.6959 (m-10) REVERT: G 182 SER cc_start: 0.8422 (p) cc_final: 0.7742 (t) REVERT: G 201 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8026 (m) REVERT: G 204 ASP cc_start: 0.7657 (t70) cc_final: 0.7266 (t0) REVERT: G 223 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7925 (mtmm) REVERT: G 257 LYS cc_start: 0.8916 (mttt) cc_final: 0.8497 (mttm) REVERT: G 258 ARG cc_start: 0.6935 (mtt180) cc_final: 0.6561 (mtt180) REVERT: G 272 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8572 (mm) REVERT: G 277 MET cc_start: 0.8113 (mmm) cc_final: 0.7649 (mmm) REVERT: G 283 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6868 (mm-30) REVERT: G 288 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7167 (tpt170) REVERT: G 290 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7600 (mtp85) REVERT: G 293 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6964 (tm-30) REVERT: G 294 ARG cc_start: 0.5344 (tmt-80) cc_final: 0.4198 (tmt170) REVERT: G 312 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 318 LEU cc_start: 0.8959 (tp) cc_final: 0.8616 (tp) REVERT: G 327 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 338 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7979 (mp) REVERT: G 342 GLU cc_start: 0.7947 (mp0) cc_final: 0.7435 (mp0) REVERT: G 344 GLU cc_start: 0.8208 (tp30) cc_final: 0.6663 (tp30) REVERT: G 347 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8219 (tm-30) REVERT: G 349 PHE cc_start: 0.8918 (t80) cc_final: 0.8454 (t80) REVERT: G 350 PHE cc_start: 0.9058 (m-10) cc_final: 0.8821 (m-80) REVERT: G 355 MET cc_start: 0.8043 (tpp) cc_final: 0.7126 (tpp) REVERT: G 359 LEU cc_start: 0.8939 (mt) cc_final: 0.8519 (mm) REVERT: G 417 ARG cc_start: 0.8739 (mtm110) cc_final: 0.8379 (mtm-85) REVERT: G 419 CYS cc_start: 0.8591 (m) cc_final: 0.8080 (m) REVERT: G 423 PHE cc_start: 0.8661 (t80) cc_final: 0.8216 (t80) REVERT: G 425 CYS cc_start: 0.8840 (m) cc_final: 0.8522 (m) REVERT: G 426 TYR cc_start: 0.8652 (t80) cc_final: 0.8408 (t80) REVERT: G 429 GLN cc_start: 0.8425 (tt0) cc_final: 0.8046 (tt0) REVERT: G 432 MET cc_start: 0.7862 (mmm) cc_final: 0.7579 (mmm) REVERT: G 437 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8133 (tm-30) REVERT: G 445 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8512 (mptp) REVERT: G 449 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7670 (mmmm) REVERT: G 453 GLN cc_start: 0.8292 (mt0) cc_final: 0.7810 (mp10) REVERT: G 456 LYS cc_start: 0.9256 (tmtm) cc_final: 0.8797 (tmtm) REVERT: G 458 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7946 (mm) REVERT: G 478 GLU cc_start: 0.8532 (pm20) cc_final: 0.8181 (pm20) REVERT: G 482 LYS cc_start: 0.8461 (tptp) cc_final: 0.7878 (tptp) REVERT: G 490 ASP cc_start: 0.8007 (p0) cc_final: 0.7652 (p0) REVERT: G 495 SER cc_start: 0.8732 (m) cc_final: 0.8251 (p) REVERT: G 497 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8564 (mm) REVERT: G 498 GLN cc_start: 0.8633 (tp40) cc_final: 0.8261 (tp40) REVERT: G 501 ARG cc_start: 0.8638 (ttp-170) cc_final: 0.8378 (ttm170) REVERT: G 502 ASN cc_start: 0.8172 (t0) cc_final: 0.7218 (t0) REVERT: G 504 ILE cc_start: 0.8686 (mm) cc_final: 0.8280 (mm) REVERT: G 506 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7571 (mm-30) REVERT: G 507 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8064 (mmm160) REVERT: G 518 LEU cc_start: 0.8124 (mt) cc_final: 0.7813 (mt) REVERT: G 540 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8475 (mm) REVERT: F 167 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5963 (pt) REVERT: F 173 PHE cc_start: 0.7920 (m-80) cc_final: 0.7617 (m-80) REVERT: F 175 GLN cc_start: 0.7449 (tm130) cc_final: 0.7113 (tm-30) REVERT: F 176 ASN cc_start: 0.8280 (t0) cc_final: 0.8028 (m110) REVERT: F 177 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7671 (m) REVERT: F 178 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8204 (mmmt) REVERT: F 191 ASP cc_start: 0.8421 (p0) cc_final: 0.8141 (p0) REVERT: F 192 LYS cc_start: 0.8676 (mmtt) cc_final: 0.7988 (mmtt) REVERT: F 193 GLN cc_start: 0.8690 (mm110) cc_final: 0.8421 (mm110) REVERT: F 194 LEU cc_start: 0.8702 (mt) cc_final: 0.8439 (mm) REVERT: F 197 ARG cc_start: 0.7659 (ptp-170) cc_final: 0.7311 (ptp-110) REVERT: F 198 GLN cc_start: 0.8328 (pm20) cc_final: 0.7828 (tp40) REVERT: F 215 PHE cc_start: 0.6743 (m-80) cc_final: 0.6441 (m-80) REVERT: F 271 ASN cc_start: 0.8587 (p0) cc_final: 0.8281 (p0) REVERT: F 277 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7958 (mtt) REVERT: F 284 LEU cc_start: 0.6999 (mt) cc_final: 0.6376 (tt) REVERT: F 322 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7107 (mt-10) REVERT: F 325 ASP cc_start: 0.8097 (m-30) cc_final: 0.7577 (m-30) REVERT: F 333 MET cc_start: 0.7780 (tpp) cc_final: 0.6862 (tpp) REVERT: F 334 MET cc_start: 0.8257 (tpt) cc_final: 0.7886 (tpt) REVERT: F 346 MET cc_start: 0.7698 (mtt) cc_final: 0.6906 (mtt) REVERT: F 347 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8016 (pp30) REVERT: F 349 PHE cc_start: 0.8695 (t80) cc_final: 0.7860 (t80) REVERT: F 355 MET cc_start: 0.8160 (tpp) cc_final: 0.7296 (tpp) REVERT: F 356 GLN cc_start: 0.8575 (tt0) cc_final: 0.8090 (tm-30) REVERT: F 357 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8028 (ttt-90) REVERT: F 358 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8115 (mtpp) REVERT: F 360 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8346 (mt-10) REVERT: F 369 GLN cc_start: 0.6853 (tm-30) cc_final: 0.6008 (tm-30) REVERT: F 373 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7806 (ttp80) REVERT: F 394 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.6978 (t-90) REVERT: F 419 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8349 (p) REVERT: F 422 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8368 (mp) REVERT: F 427 THR cc_start: 0.8856 (p) cc_final: 0.8545 (t) REVERT: F 437 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7793 (mm110) REVERT: F 448 GLN cc_start: 0.8773 (mt0) cc_final: 0.8266 (mt0) REVERT: F 464 GLU cc_start: 0.8078 (tp30) cc_final: 0.7513 (tp30) REVERT: F 484 LEU cc_start: 0.8518 (mt) cc_final: 0.8315 (mm) REVERT: F 494 GLN cc_start: 0.8454 (mt0) cc_final: 0.8037 (mt0) REVERT: F 495 SER cc_start: 0.8000 (t) cc_final: 0.7113 (p) REVERT: F 498 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7898 (tp-100) REVERT: F 499 ASN cc_start: 0.8277 (m-40) cc_final: 0.7793 (m110) REVERT: F 501 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8131 (ttm110) REVERT: F 502 ASN cc_start: 0.7851 (t0) cc_final: 0.7367 (t0) REVERT: F 505 LEU cc_start: 0.8754 (mm) cc_final: 0.8498 (mm) REVERT: F 528 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.5807 (mtm180) REVERT: F 534 LEU cc_start: 0.8738 (mt) cc_final: 0.8493 (mm) REVERT: F 539 TYR cc_start: 0.8205 (t80) cc_final: 0.7456 (t80) REVERT: F 575 HIS cc_start: 0.8723 (m90) cc_final: 0.7902 (m90) REVERT: F 576 ARG cc_start: 0.7540 (mmp80) cc_final: 0.7092 (mtm-85) REVERT: F 581 ASN cc_start: 0.8305 (t0) cc_final: 0.7780 (t0) REVERT: F 583 GLN cc_start: 0.8780 (mm110) cc_final: 0.8556 (mm110) REVERT: F 587 GLU cc_start: 0.8421 (tt0) cc_final: 0.8120 (tt0) REVERT: F 611 LYS cc_start: 0.8562 (pttt) cc_final: 0.8117 (mmtp) REVERT: F 616 LEU cc_start: 0.8183 (tt) cc_final: 0.7958 (mm) REVERT: F 617 TRP cc_start: 0.8194 (t60) cc_final: 0.7800 (t60) REVERT: F 621 TYR cc_start: 0.8567 (t80) cc_final: 0.8160 (t80) REVERT: F 623 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7651 (ttp80) REVERT: F 628 GLU cc_start: 0.8284 (pt0) cc_final: 0.7550 (pt0) REVERT: F 646 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7995 (t0) REVERT: F 649 LEU cc_start: 0.8706 (mt) cc_final: 0.8302 (mt) REVERT: F 672 GLU cc_start: 0.8205 (pp20) cc_final: 0.7803 (pp20) REVERT: F 676 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7821 (ttm-80) outliers start: 43 outliers final: 25 residues processed: 396 average time/residue: 0.3300 time to fit residues: 165.7390 Evaluate side-chains 422 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 380 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 459 TRP Chi-restraints excluded: chain G residue 497 LEU Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 CYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 419 CYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 542 GLN Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 646 ASN Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 664 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS F 313 GLN F 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098467 restraints weight = 15277.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102223 restraints weight = 7796.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104741 restraints weight = 4772.892| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6998 Z= 0.155 Angle : 0.804 11.891 9480 Z= 0.398 Chirality : 0.046 0.175 1059 Planarity : 0.004 0.039 1227 Dihedral : 4.774 50.086 936 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.74 % Allowed : 34.85 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 835 helix: 1.35 (0.24), residues: 474 sheet: -0.74 (1.80), residues: 12 loop : -1.25 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 459 HIS 0.014 0.001 HIS F 264 PHE 0.024 0.001 PHE F 423 TYR 0.029 0.001 TYR F 546 ARG 0.010 0.000 ARG F 636 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 342) hydrogen bonds : angle 4.49139 ( 984) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.56672 ( 4) covalent geometry : bond 0.00344 ( 6996) covalent geometry : angle 0.80386 ( 9476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.51 seconds wall clock time: 74 minutes 33.01 seconds (4473.01 seconds total)