Starting phenix.real_space_refine on Wed Sep 17 08:03:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivw_60935/09_2025/9ivw_60935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivw_60935/09_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_60935/09_2025/9ivw_60935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivw_60935/09_2025/9ivw_60935.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivw_60935/09_2025/9ivw_60935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivw_60935/09_2025/9ivw_60935.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.82, per 1000 atoms: 0.27 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: 0.51 Conformation dependent library (CDL) restraints added in 430.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.16 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: 0.87 Time building geometry restraints manager: 0.69 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: 0.900 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG F 417 TYR 0.016 0.001 TYR G 546 PHE 0.021 0.001 PHE G 503 TRP 0.026 0.002 TRP G 459 HIS 0.005 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 6996) covalent geometry : angle 1.05992 ( 9476) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.73391 ( 4) hydrogen bonds : bond 0.17027 ( 342) hydrogen bonds : angle 6.41121 ( 984) *********************** 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 : 0.192 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: 0.1132 time to fit residues: 58.2480 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 : 0.244 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.121089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102388 restraints weight = 15223.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106306 restraints weight = 7872.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.108960 restraints weight = 4856.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110796 restraints weight = 3358.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112098 restraints weight = 2515.444| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6998 Z= 0.163 Angle : 0.774 11.610 9480 Z= 0.383 Chirality : 0.046 0.168 1059 Planarity : 0.005 0.042 1227 Dihedral : 8.006 64.730 976 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.87 % Allowed : 25.77 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.29), residues: 835 helix: 1.03 (0.24), residues: 463 sheet: -1.51 (1.58), residues: 12 loop : -1.15 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 417 TYR 0.018 0.002 TYR F 546 PHE 0.013 0.001 PHE F 423 TRP 0.013 0.002 TRP F 317 HIS 0.004 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6996) covalent geometry : angle 0.77374 ( 9476) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.91616 ( 4) hydrogen bonds : bond 0.04876 ( 342) hydrogen bonds : angle 4.80107 ( 984) *********************** 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: 44 poor density : 383 time to evaluate : 0.210 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 181 LEU cc_start: 0.8521 (mp) cc_final: 0.7908 (pt) REVERT: G 182 SER cc_start: 0.8394 (p) cc_final: 0.7707 (t) REVERT: G 184 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7652 (ttp80) REVERT: G 187 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.7497 (mpt180) REVERT: G 193 GLN cc_start: 0.8738 (mp10) cc_final: 0.8449 (mp10) REVERT: G 204 ASP cc_start: 0.7648 (t70) cc_final: 0.7298 (t0) REVERT: G 223 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7919 (mtmm) REVERT: G 277 MET cc_start: 0.7948 (mmm) cc_final: 0.7730 (mmm) REVERT: G 284 LEU cc_start: 0.8568 (tp) cc_final: 0.8355 (tt) REVERT: G 285 ILE cc_start: 0.8386 (mm) cc_final: 0.8135 (mm) REVERT: G 288 ARG cc_start: 0.7592 (tpp-160) cc_final: 0.7033 (tpm170) REVERT: G 290 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7432 (mtp85) REVERT: G 299 GLN cc_start: 0.8592 (mp10) cc_final: 0.8365 (mp10) REVERT: G 312 GLU cc_start: 0.7913 (tm-30) cc_final: 0.6617 (tm-30) REVERT: G 316 ARG cc_start: 0.8737 (mtp180) cc_final: 0.8193 (mtp180) REVERT: G 327 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7878 (tm-30) REVERT: G 328 GLU cc_start: 0.8629 (pp20) cc_final: 0.7915 (pp20) REVERT: G 331 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8460 (ptmt) REVERT: G 333 MET cc_start: 0.8422 (ptm) cc_final: 0.7797 (ptp) REVERT: G 344 GLU cc_start: 0.8091 (tp30) cc_final: 0.6969 (tp30) REVERT: G 348 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8521 (mmt90) REVERT: G 349 PHE cc_start: 0.8943 (t80) cc_final: 0.8609 (t80) REVERT: G 355 MET cc_start: 0.7474 (tpp) cc_final: 0.6755 (tpp) REVERT: G 359 LEU cc_start: 0.8991 (mt) cc_final: 0.8434 (mm) REVERT: G 408 LYS cc_start: 0.8267 (tppt) cc_final: 0.7260 (tppt) REVERT: G 412 ARG cc_start: 0.8461 (ttt180) cc_final: 0.7997 (ttp-170) REVERT: G 413 ARG cc_start: 0.8634 (mpp80) cc_final: 0.8432 (mpp80) REVERT: G 417 ARG cc_start: 0.8725 (mtm110) cc_final: 0.8399 (mtm-85) REVERT: G 418 ASP cc_start: 0.8408 (t0) cc_final: 0.8133 (t70) REVERT: G 419 CYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8406 (m) REVERT: G 420 VAL cc_start: 0.9095 (p) cc_final: 0.8655 (p) REVERT: G 421 TYR cc_start: 0.8174 (t80) cc_final: 0.7641 (t80) REVERT: G 423 PHE cc_start: 0.8613 (t80) cc_final: 0.8338 (t80) REVERT: G 424 LEU cc_start: 0.8926 (mt) cc_final: 0.8698 (mt) REVERT: G 425 CYS cc_start: 0.8930 (m) cc_final: 0.8483 (m) REVERT: G 426 TYR cc_start: 0.8567 (t80) cc_final: 0.8193 (t80) REVERT: G 428 TRP cc_start: 0.8756 (t-100) cc_final: 0.8517 (t-100) REVERT: G 429 GLN cc_start: 0.8340 (tt0) cc_final: 0.7928 (tt0) REVERT: G 432 MET cc_start: 0.7889 (mmm) cc_final: 0.7342 (mmm) REVERT: G 443 ASN cc_start: 0.8570 (m110) cc_final: 0.8072 (m110) REVERT: G 444 LEU cc_start: 0.8789 (mm) cc_final: 0.8580 (mm) REVERT: G 445 LYS cc_start: 0.8784 (mptp) cc_final: 0.8361 (mptp) REVERT: G 446 GLU cc_start: 0.7546 (tt0) cc_final: 0.7009 (pt0) REVERT: G 447 LEU cc_start: 0.8700 (mp) cc_final: 0.8428 (mp) REVERT: G 448 GLN cc_start: 0.8344 (mt0) cc_final: 0.7239 (mt0) REVERT: G 452 LYS cc_start: 0.8532 (mttm) cc_final: 0.7886 (mttm) REVERT: G 453 GLN cc_start: 0.8061 (mt0) cc_final: 0.7686 (mp10) REVERT: G 465 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8627 (mmm-85) REVERT: G 470 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8202 (m-70) REVERT: G 478 GLU cc_start: 0.8449 (pm20) cc_final: 0.8136 (pm20) REVERT: G 482 LYS cc_start: 0.8551 (tptp) cc_final: 0.8067 (tptp) REVERT: G 486 GLN cc_start: 0.7749 (mm110) cc_final: 0.7404 (mm110) REVERT: G 488 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7380 (tm) REVERT: G 495 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8109 (p) REVERT: G 497 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8635 (mm) REVERT: G 498 GLN cc_start: 0.8513 (tp40) cc_final: 0.8032 (tp40) REVERT: G 501 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8279 (ttp-170) REVERT: G 503 PHE cc_start: 0.8707 (t80) cc_final: 0.8329 (t80) REVERT: G 504 ILE cc_start: 0.8703 (mm) cc_final: 0.8394 (mm) REVERT: G 506 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 510 ILE cc_start: 0.8146 (mm) cc_final: 0.7906 (mm) REVERT: G 518 LEU cc_start: 0.8075 (mt) cc_final: 0.7368 (pp) REVERT: G 554 MET cc_start: 0.6474 (tmm) cc_final: 0.5742 (tmm) REVERT: F 191 ASP cc_start: 0.8640 (p0) cc_final: 0.8043 (p0) REVERT: F 192 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8214 (mmtt) REVERT: F 194 LEU cc_start: 0.8922 (mt) cc_final: 0.8455 (mm) REVERT: F 198 GLN cc_start: 0.8269 (pm20) cc_final: 0.7327 (tp40) REVERT: F 204 ASP cc_start: 0.8100 (p0) cc_final: 0.7896 (p0) REVERT: F 215 PHE cc_start: 0.6593 (m-80) cc_final: 0.6249 (m-80) REVERT: F 277 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: F 322 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7141 (mt-10) REVERT: F 325 ASP cc_start: 0.7833 (m-30) cc_final: 0.7078 (m-30) REVERT: F 333 MET cc_start: 0.7553 (tpp) cc_final: 0.7311 (mpp) REVERT: F 334 MET cc_start: 0.8181 (tpt) cc_final: 0.7263 (tpt) REVERT: F 338 LEU cc_start: 0.8854 (tp) cc_final: 0.8611 (mt) REVERT: F 346 MET cc_start: 0.7659 (mtt) cc_final: 0.7189 (mtt) REVERT: F 347 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7642 (tp-100) REVERT: F 349 PHE cc_start: 0.8600 (t80) cc_final: 0.7942 (t80) REVERT: F 355 MET cc_start: 0.8137 (tpp) cc_final: 0.7186 (tpp) REVERT: F 357 ARG cc_start: 0.8444 (ttt180) cc_final: 0.7985 (ttt-90) REVERT: F 363 LEU cc_start: 0.8836 (mm) cc_final: 0.8437 (mt) REVERT: F 366 THR cc_start: 0.8731 (t) cc_final: 0.8423 (p) REVERT: F 369 GLN cc_start: 0.6571 (tm-30) cc_final: 0.6188 (tm-30) REVERT: F 371 TYR cc_start: 0.8160 (p90) cc_final: 0.7949 (p90) REVERT: F 373 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7527 (ttp80) REVERT: F 374 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7705 (mm-40) REVERT: F 392 ILE cc_start: 0.7676 (tp) cc_final: 0.7334 (tp) REVERT: F 405 SER cc_start: 0.8763 (t) cc_final: 0.8518 (p) REVERT: F 423 PHE cc_start: 0.8639 (t80) cc_final: 0.8421 (t80) REVERT: F 429 GLN cc_start: 0.8747 (mt0) cc_final: 0.8393 (mt0) REVERT: F 435 TRP cc_start: 0.8229 (t60) cc_final: 0.7981 (t60) REVERT: F 437 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7758 (mm110) REVERT: F 448 GLN cc_start: 0.8832 (mt0) cc_final: 0.8297 (mt0) REVERT: F 464 GLU cc_start: 0.7800 (tp30) cc_final: 0.7362 (tp30) REVERT: F 485 GLN cc_start: 0.7439 (mt0) cc_final: 0.7154 (pt0) REVERT: F 495 SER cc_start: 0.8211 (t) cc_final: 0.7707 (p) REVERT: F 498 GLN cc_start: 0.8082 (tm-30) cc_final: 0.6782 (tp-100) REVERT: F 499 ASN cc_start: 0.8361 (m-40) cc_final: 0.8151 (m-40) REVERT: F 501 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8115 (ttp80) REVERT: F 502 ASN cc_start: 0.7958 (t0) cc_final: 0.7504 (t0) REVERT: F 528 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.4712 (mtm180) REVERT: F 538 CYS cc_start: 0.8371 (m) cc_final: 0.7712 (m) REVERT: F 539 TYR cc_start: 0.7994 (t80) cc_final: 0.7328 (t80) REVERT: F 575 HIS cc_start: 0.8666 (m90) cc_final: 0.8386 (m90) REVERT: F 581 ASN cc_start: 0.8211 (t0) cc_final: 0.7995 (t0) REVERT: F 583 GLN cc_start: 0.8718 (mm110) cc_final: 0.8517 (mm110) REVERT: F 587 GLU cc_start: 0.8093 (tt0) cc_final: 0.7759 (tt0) REVERT: F 611 LYS cc_start: 0.8436 (pttt) cc_final: 0.8141 (pttt) REVERT: F 616 LEU cc_start: 0.8248 (tt) cc_final: 0.7987 (mm) REVERT: F 617 TRP cc_start: 0.8211 (t60) cc_final: 0.7854 (t60) REVERT: F 628 GLU cc_start: 0.8243 (pt0) cc_final: 0.7797 (pt0) REVERT: F 676 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7761 (tpp80) REVERT: F 684 ASP cc_start: 0.8338 (t0) cc_final: 0.7718 (p0) outliers start: 44 outliers final: 26 residues processed: 398 average time/residue: 0.1130 time to fit residues: 55.7849 Evaluate side-chains 407 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 470 HIS 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 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 82 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.0040 chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 overall best weight: 1.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 186 ASN F 193 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN F 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.117299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099029 restraints weight = 15066.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102803 restraints weight = 7789.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105328 restraints weight = 4803.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.107098 restraints weight = 3312.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108326 restraints weight = 2485.603| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6998 Z= 0.190 Angle : 0.749 11.244 9480 Z= 0.374 Chirality : 0.046 0.161 1059 Planarity : 0.005 0.058 1227 Dihedral : 6.257 57.102 953 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 6.01 % Allowed : 27.37 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.30), residues: 835 helix: 1.05 (0.24), residues: 478 sheet: None (None), residues: 0 loop : -1.14 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 330 TYR 0.025 0.002 TYR F 546 PHE 0.019 0.001 PHE F 174 TRP 0.016 0.002 TRP F 459 HIS 0.004 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6996) covalent geometry : angle 0.74879 ( 9476) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.60331 ( 4) hydrogen bonds : bond 0.04411 ( 342) hydrogen bonds : angle 4.66779 ( 984) *********************** 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 430 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 385 time to evaluate : 0.260 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: 0.8459 (mp) cc_final: 0.7897 (pt) REVERT: G 182 SER cc_start: 0.8346 (p) cc_final: 0.7911 (t) REVERT: G 192 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8741 (mtpt) REVERT: G 201 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8159 (m) REVERT: G 204 ASP cc_start: 0.7722 (t70) cc_final: 0.7374 (t0) REVERT: G 223 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7871 (mtmm) REVERT: G 244 VAL cc_start: 0.8441 (m) cc_final: 0.8212 (p) REVERT: G 252 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8006 (ttt-90) REVERT: G 257 LYS cc_start: 0.8889 (mttt) cc_final: 0.8082 (mttm) REVERT: G 258 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6728 (mtt180) REVERT: G 272 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8432 (mm) REVERT: G 277 MET cc_start: 0.7945 (mmm) cc_final: 0.7713 (mmm) REVERT: G 288 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7105 (tpt170) REVERT: G 290 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7478 (mtp85) REVERT: G 293 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6759 (tm-30) REVERT: G 294 ARG cc_start: 0.6033 (tmt-80) cc_final: 0.5591 (tmt-80) REVERT: G 299 GLN cc_start: 0.8586 (mp10) cc_final: 0.8299 (mp10) REVERT: G 312 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7696 (tm-30) REVERT: G 318 LEU cc_start: 0.8839 (tp) cc_final: 0.8448 (tp) REVERT: G 327 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7861 (tm-30) REVERT: G 333 MET cc_start: 0.8468 (ptm) cc_final: 0.8053 (ptp) REVERT: G 342 GLU cc_start: 0.8019 (mp0) cc_final: 0.7428 (mp0) REVERT: G 344 GLU cc_start: 0.8244 (tp30) cc_final: 0.7034 (tp30) REVERT: G 346 MET cc_start: 0.8693 (mtt) cc_final: 0.8480 (mtt) REVERT: G 348 ARG cc_start: 0.8798 (mtt180) cc_final: 0.8457 (mmt90) REVERT: G 349 PHE cc_start: 0.8986 (t80) cc_final: 0.8606 (t80) REVERT: G 355 MET cc_start: 0.7799 (tpp) cc_final: 0.6820 (tpp) REVERT: G 359 LEU cc_start: 0.9059 (mt) cc_final: 0.8354 (mm) REVERT: G 417 ARG cc_start: 0.8726 (mtm110) cc_final: 0.8351 (mtm-85) REVERT: G 419 CYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8321 (m) REVERT: G 420 VAL cc_start: 0.9061 (p) cc_final: 0.8702 (p) REVERT: G 421 TYR cc_start: 0.8232 (t80) cc_final: 0.7699 (t80) REVERT: G 423 PHE cc_start: 0.8610 (t80) cc_final: 0.8262 (t80) REVERT: G 424 LEU cc_start: 0.8949 (mt) cc_final: 0.8685 (mt) REVERT: G 425 CYS cc_start: 0.8885 (m) cc_final: 0.8489 (m) REVERT: G 426 TYR cc_start: 0.8513 (t80) cc_final: 0.8296 (t80) REVERT: G 428 TRP cc_start: 0.8798 (t-100) cc_final: 0.8556 (t-100) REVERT: G 429 GLN cc_start: 0.8292 (tt0) cc_final: 0.7940 (tt0) REVERT: G 432 MET cc_start: 0.7913 (mmm) cc_final: 0.7363 (mmm) REVERT: G 442 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7362 (mtp-110) REVERT: G 443 ASN cc_start: 0.8641 (m110) cc_final: 0.8148 (m-40) REVERT: G 444 LEU cc_start: 0.8794 (mm) cc_final: 0.8589 (mm) REVERT: G 445 LYS cc_start: 0.8765 (mptp) cc_final: 0.8358 (mptp) REVERT: G 446 GLU cc_start: 0.7679 (tt0) cc_final: 0.7125 (pt0) REVERT: G 448 GLN cc_start: 0.8409 (mt0) cc_final: 0.7293 (mt0) REVERT: G 452 LYS cc_start: 0.8622 (mttm) cc_final: 0.7971 (mttm) REVERT: G 453 GLN cc_start: 0.8188 (mt0) cc_final: 0.7809 (mp10) REVERT: G 459 TRP cc_start: 0.8376 (m100) cc_final: 0.7984 (m100) REVERT: G 464 GLU cc_start: 0.8307 (mp0) cc_final: 0.8080 (mp0) REVERT: G 478 GLU cc_start: 0.8483 (pm20) cc_final: 0.8130 (pm20) REVERT: G 482 LYS cc_start: 0.8525 (tptp) cc_final: 0.7676 (tptp) REVERT: G 483 THR cc_start: 0.8846 (t) cc_final: 0.8585 (p) REVERT: G 486 GLN cc_start: 0.7736 (mm110) cc_final: 0.6906 (mm110) REVERT: G 495 SER cc_start: 0.8786 (m) cc_final: 0.8206 (p) REVERT: G 497 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8552 (mm) REVERT: G 498 GLN cc_start: 0.8677 (tp40) cc_final: 0.7497 (tp40) REVERT: G 501 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8048 (ptp-110) REVERT: G 502 ASN cc_start: 0.8286 (t0) cc_final: 0.7303 (t0) REVERT: G 504 ILE cc_start: 0.8694 (mm) cc_final: 0.8397 (mm) REVERT: G 506 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7690 (mm-30) REVERT: G 507 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8354 (mmm160) REVERT: G 540 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8435 (mm) REVERT: G 554 MET cc_start: 0.6678 (tmm) cc_final: 0.6377 (tmm) REVERT: F 167 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5648 (mp) REVERT: F 176 ASN cc_start: 0.8395 (m-40) cc_final: 0.7974 (m-40) REVERT: F 178 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8134 (mmmt) REVERT: F 191 ASP cc_start: 0.8607 (p0) cc_final: 0.7865 (p0) REVERT: F 192 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8100 (mmtt) REVERT: F 193 GLN cc_start: 0.8770 (mm110) cc_final: 0.8481 (mm-40) REVERT: F 194 LEU cc_start: 0.8871 (mt) cc_final: 0.8563 (mm) REVERT: F 198 GLN cc_start: 0.8339 (pm20) cc_final: 0.7657 (tp40) REVERT: F 204 ASP cc_start: 0.8183 (p0) cc_final: 0.7948 (p0) REVERT: F 215 PHE cc_start: 0.6669 (m-80) cc_final: 0.6357 (m-80) REVERT: F 271 ASN cc_start: 0.8206 (p0) cc_final: 0.7849 (p0) REVERT: F 277 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7893 (mtt) REVERT: F 313 GLN cc_start: 0.8793 (mp-120) cc_final: 0.8271 (pt0) REVERT: F 322 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7188 (mt-10) REVERT: F 325 ASP cc_start: 0.7954 (m-30) cc_final: 0.7240 (m-30) REVERT: F 327 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8180 (mm-30) REVERT: F 329 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7432 (tpp80) REVERT: F 333 MET cc_start: 0.7833 (tpp) cc_final: 0.7242 (mpp) REVERT: F 334 MET cc_start: 0.8231 (tpt) cc_final: 0.7935 (tpt) REVERT: F 346 MET cc_start: 0.7739 (mtt) cc_final: 0.7012 (mtt) REVERT: F 349 PHE cc_start: 0.8650 (t80) cc_final: 0.8169 (t80) REVERT: F 355 MET cc_start: 0.8228 (tpp) cc_final: 0.7114 (tpp) REVERT: F 356 GLN cc_start: 0.8456 (tt0) cc_final: 0.7889 (tm-30) REVERT: F 357 ARG cc_start: 0.8469 (ttt180) cc_final: 0.8007 (ttt-90) REVERT: F 358 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8108 (mtpp) REVERT: F 363 LEU cc_start: 0.8805 (mm) cc_final: 0.8480 (mt) REVERT: F 369 GLN cc_start: 0.6531 (tm-30) cc_final: 0.5824 (tm-30) REVERT: F 373 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7713 (ttp80) REVERT: F 374 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7797 (mm-40) REVERT: F 383 LEU cc_start: 0.8524 (mm) cc_final: 0.8239 (mt) REVERT: F 405 SER cc_start: 0.8765 (t) cc_final: 0.8523 (p) REVERT: F 419 CYS cc_start: 0.8856 (m) cc_final: 0.8332 (p) REVERT: F 423 PHE cc_start: 0.8686 (t80) cc_final: 0.8397 (t80) REVERT: F 429 GLN cc_start: 0.8723 (mt0) cc_final: 0.8363 (mt0) REVERT: F 437 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7786 (mm110) REVERT: F 446 GLU cc_start: 0.8415 (tt0) cc_final: 0.7861 (pt0) REVERT: F 448 GLN cc_start: 0.8840 (mt0) cc_final: 0.8290 (mt0) REVERT: F 464 GLU cc_start: 0.7965 (tp30) cc_final: 0.7559 (tp30) REVERT: F 485 GLN cc_start: 0.7571 (mt0) cc_final: 0.7231 (mt0) REVERT: F 495 SER cc_start: 0.8177 (t) cc_final: 0.7750 (p) REVERT: F 498 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7693 (tp-100) REVERT: F 499 ASN cc_start: 0.8385 (m-40) cc_final: 0.8150 (m-40) REVERT: F 502 ASN cc_start: 0.7978 (t0) cc_final: 0.6985 (t0) REVERT: F 506 GLU cc_start: 0.7569 (pt0) cc_final: 0.6767 (pt0) REVERT: F 528 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.5315 (ttp-170) REVERT: F 538 CYS cc_start: 0.8421 (m) cc_final: 0.7816 (m) REVERT: F 539 TYR cc_start: 0.8088 (t80) cc_final: 0.7349 (t80) REVERT: F 575 HIS cc_start: 0.8740 (m90) cc_final: 0.8481 (m90) REVERT: F 576 ARG cc_start: 0.7533 (mmp80) cc_final: 0.7162 (mtm-85) REVERT: F 581 ASN cc_start: 0.8248 (t0) cc_final: 0.7862 (t0) REVERT: F 583 GLN cc_start: 0.8774 (mm110) cc_final: 0.8551 (mm110) REVERT: F 587 GLU cc_start: 0.8167 (tt0) cc_final: 0.7829 (tt0) REVERT: F 611 LYS cc_start: 0.8516 (pttt) cc_final: 0.8070 (mmtp) REVERT: F 616 LEU cc_start: 0.8234 (tt) cc_final: 0.7998 (mm) REVERT: F 617 TRP cc_start: 0.8244 (t60) cc_final: 0.7824 (t60) REVERT: F 621 TYR cc_start: 0.8643 (t80) cc_final: 0.8219 (t80) REVERT: F 623 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7502 (ttp80) REVERT: F 628 GLU cc_start: 0.8287 (pt0) cc_final: 0.7819 (pt0) REVERT: F 637 PHE cc_start: 0.8299 (m-80) cc_final: 0.8095 (m-80) REVERT: F 672 GLU cc_start: 0.8291 (pp20) cc_final: 0.7914 (pp20) REVERT: F 676 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7838 (ttm-80) REVERT: F 684 ASP cc_start: 0.8223 (t0) cc_final: 0.7416 (t0) outliers start: 45 outliers final: 14 residues processed: 402 average time/residue: 0.1054 time to fit residues: 53.3932 Evaluate side-chains 404 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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 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 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN ** F 313 GLN ** 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 = 0.3738 r_free = 0.3738 target = 0.116291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097876 restraints weight = 15213.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101698 restraints weight = 7763.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104265 restraints weight = 4755.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106118 restraints weight = 3268.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107292 restraints weight = 2434.432| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6998 Z= 0.142 Angle : 0.705 9.385 9480 Z= 0.350 Chirality : 0.045 0.185 1059 Planarity : 0.005 0.045 1227 Dihedral : 4.941 54.414 937 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.54 % Allowed : 28.30 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.30), residues: 835 helix: 1.27 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 636 TYR 0.025 0.002 TYR F 546 PHE 0.015 0.001 PHE G 503 TRP 0.016 0.002 TRP F 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6996) covalent geometry : angle 0.70463 ( 9476) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.72050 ( 4) hydrogen bonds : bond 0.04009 ( 342) hydrogen bonds : angle 4.50015 ( 984) *********************** 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 440 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 0.267 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: G 181 LEU cc_start: 0.8505 (mp) cc_final: 0.7888 (pt) REVERT: G 182 SER cc_start: 0.8324 (p) cc_final: 0.7885 (t) REVERT: G 193 GLN cc_start: 0.8735 (mp10) cc_final: 0.8299 (mp10) REVERT: G 201 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8127 (m) REVERT: G 204 ASP cc_start: 0.7689 (t70) cc_final: 0.7327 (t0) REVERT: G 223 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7886 (mtmm) REVERT: G 257 LYS cc_start: 0.8885 (mttt) cc_final: 0.8442 (mttt) REVERT: G 258 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6675 (mtt180) REVERT: G 272 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8607 (mm) REVERT: G 277 MET cc_start: 0.7948 (mmm) cc_final: 0.7662 (mmm) REVERT: G 288 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7194 (tpt170) REVERT: G 290 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7495 (mtp85) REVERT: G 293 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6987 (tm-30) REVERT: G 294 ARG cc_start: 0.6123 (tmt-80) cc_final: 0.5275 (tmt-80) REVERT: G 299 GLN cc_start: 0.8503 (mp10) cc_final: 0.8239 (mp10) REVERT: G 312 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7756 (tm-30) REVERT: G 314 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8221 (pp) REVERT: G 318 LEU cc_start: 0.8857 (tp) cc_final: 0.8450 (tp) REVERT: G 327 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 333 MET cc_start: 0.8493 (ptm) cc_final: 0.7565 (ptp) REVERT: G 342 GLU cc_start: 0.7872 (mp0) cc_final: 0.7339 (mp0) REVERT: G 344 GLU cc_start: 0.8225 (tp30) cc_final: 0.6897 (tp30) REVERT: G 348 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8295 (mmt90) REVERT: G 349 PHE cc_start: 0.8972 (t80) cc_final: 0.8589 (t80) REVERT: G 355 MET cc_start: 0.7820 (tpp) cc_final: 0.6858 (tpp) REVERT: G 359 LEU cc_start: 0.8988 (mt) cc_final: 0.8353 (mm) REVERT: G 413 ARG cc_start: 0.8505 (mpp80) cc_final: 0.8199 (mpp80) REVERT: G 417 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8363 (mtm-85) REVERT: G 419 CYS cc_start: 0.8676 (m) cc_final: 0.8183 (m) REVERT: G 421 TYR cc_start: 0.8224 (t80) cc_final: 0.7588 (t80) REVERT: G 422 LEU cc_start: 0.8757 (mt) cc_final: 0.8538 (mt) REVERT: G 423 PHE cc_start: 0.8603 (t80) cc_final: 0.8269 (t80) REVERT: G 425 CYS cc_start: 0.8866 (m) cc_final: 0.8555 (m) REVERT: G 426 TYR cc_start: 0.8559 (t80) cc_final: 0.8295 (t80) REVERT: G 429 GLN cc_start: 0.8310 (tt0) cc_final: 0.7976 (tt0) REVERT: G 432 MET cc_start: 0.7923 (mmm) cc_final: 0.7387 (mmm) REVERT: G 442 ARG cc_start: 0.7631 (mtp-110) cc_final: 0.7385 (mtp-110) REVERT: G 445 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8332 (mptp) REVERT: G 446 GLU cc_start: 0.7637 (tt0) cc_final: 0.7129 (pt0) REVERT: G 448 GLN cc_start: 0.8408 (mt0) cc_final: 0.7256 (mt0) REVERT: G 449 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7581 (mmmm) REVERT: G 452 LYS cc_start: 0.8638 (mttm) cc_final: 0.7934 (mttm) REVERT: G 453 GLN cc_start: 0.8263 (mt0) cc_final: 0.7830 (mp10) REVERT: G 456 LYS cc_start: 0.9272 (tmtm) cc_final: 0.8851 (tmtm) REVERT: G 459 TRP cc_start: 0.8395 (m100) cc_final: 0.8140 (m100) REVERT: G 478 GLU cc_start: 0.8494 (pm20) cc_final: 0.8135 (pm20) REVERT: G 482 LYS cc_start: 0.8481 (tptp) cc_final: 0.7623 (tptp) REVERT: G 486 GLN cc_start: 0.7680 (mm110) cc_final: 0.6812 (mm110) REVERT: G 495 SER cc_start: 0.8800 (m) cc_final: 0.8220 (p) REVERT: G 497 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8578 (mm) REVERT: G 498 GLN cc_start: 0.8693 (tp40) cc_final: 0.7600 (tp40) REVERT: G 501 ARG cc_start: 0.8680 (ttp-170) cc_final: 0.7953 (ptp-110) REVERT: G 502 ASN cc_start: 0.8226 (t0) cc_final: 0.7231 (t0) REVERT: G 504 ILE cc_start: 0.8673 (mm) cc_final: 0.8399 (mm) REVERT: G 506 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7534 (mm-30) REVERT: G 507 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8136 (mmm160) REVERT: G 540 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8476 (mm) REVERT: F 167 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5624 (mp) REVERT: F 175 GLN cc_start: 0.7064 (tm130) cc_final: 0.6814 (tm-30) REVERT: F 178 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8172 (mmmt) REVERT: F 191 ASP cc_start: 0.8530 (p0) cc_final: 0.7999 (p0) REVERT: F 192 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8054 (mmtt) REVERT: F 193 GLN cc_start: 0.8717 (mm110) cc_final: 0.8366 (mm110) REVERT: F 194 LEU cc_start: 0.8782 (mt) cc_final: 0.8509 (mm) REVERT: F 198 GLN cc_start: 0.8328 (pm20) cc_final: 0.7631 (tp40) REVERT: F 204 ASP cc_start: 0.8205 (p0) cc_final: 0.7958 (p0) REVERT: F 215 PHE cc_start: 0.6701 (m-80) cc_final: 0.6366 (m-80) REVERT: F 271 ASN cc_start: 0.8302 (p0) cc_final: 0.7906 (p0) REVERT: F 277 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7430 (mtt) REVERT: F 313 GLN cc_start: 0.8766 (mp-120) cc_final: 0.8557 (pm20) REVERT: F 322 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7051 (mt-10) REVERT: F 325 ASP cc_start: 0.7849 (m-30) cc_final: 0.7100 (m-30) REVERT: F 328 GLU cc_start: 0.8692 (pp20) cc_final: 0.8481 (pp20) REVERT: F 333 MET cc_start: 0.7850 (tpp) cc_final: 0.7480 (mpp) REVERT: F 334 MET cc_start: 0.8181 (tpt) cc_final: 0.7859 (tpt) REVERT: F 346 MET cc_start: 0.7681 (mtt) cc_final: 0.7085 (mtt) REVERT: F 349 PHE cc_start: 0.8659 (t80) cc_final: 0.7879 (t80) REVERT: F 355 MET cc_start: 0.8198 (tpp) cc_final: 0.7069 (tpp) REVERT: F 356 GLN cc_start: 0.8552 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 357 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8035 (ttt-90) REVERT: F 358 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8126 (mtpp) REVERT: F 368 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7472 (ttt-90) REVERT: F 369 GLN cc_start: 0.6691 (tm-30) cc_final: 0.5927 (tm-30) REVERT: F 373 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7709 (ttp80) REVERT: F 374 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7802 (mm-40) REVERT: F 383 LEU cc_start: 0.8646 (mm) cc_final: 0.8395 (mt) REVERT: F 394 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: F 405 SER cc_start: 0.8777 (t) cc_final: 0.8545 (p) REVERT: F 419 CYS cc_start: 0.8824 (m) cc_final: 0.8333 (p) REVERT: F 423 PHE cc_start: 0.8631 (t80) cc_final: 0.8306 (t80) REVERT: F 437 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7760 (mm110) REVERT: F 441 GLU cc_start: 0.7980 (mp0) cc_final: 0.7718 (tp30) REVERT: F 446 GLU cc_start: 0.8407 (tt0) cc_final: 0.7820 (pt0) REVERT: F 448 GLN cc_start: 0.8849 (mt0) cc_final: 0.8284 (mt0) REVERT: F 464 GLU cc_start: 0.7781 (tp30) cc_final: 0.7564 (tp30) REVERT: F 495 SER cc_start: 0.8138 (t) cc_final: 0.7651 (p) REVERT: F 498 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7537 (tp-100) REVERT: F 499 ASN cc_start: 0.8491 (m-40) cc_final: 0.8192 (m-40) REVERT: F 501 ARG cc_start: 0.8469 (ttm110) cc_final: 0.7857 (ptm160) REVERT: F 502 ASN cc_start: 0.7913 (t0) cc_final: 0.7423 (t0) REVERT: F 528 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.5342 (ttp-170) REVERT: F 539 TYR cc_start: 0.8168 (t80) cc_final: 0.7578 (t80) REVERT: F 575 HIS cc_start: 0.8736 (m90) cc_final: 0.8166 (m90) REVERT: F 576 ARG cc_start: 0.7514 (mmp80) cc_final: 0.6970 (mtm-85) REVERT: F 581 ASN cc_start: 0.8213 (t0) cc_final: 0.7811 (t0) REVERT: F 583 GLN cc_start: 0.8780 (mm110) cc_final: 0.8554 (mm110) REVERT: F 587 GLU cc_start: 0.8233 (tt0) cc_final: 0.7927 (tt0) REVERT: F 611 LYS cc_start: 0.8580 (pttt) cc_final: 0.8325 (pttt) REVERT: F 616 LEU cc_start: 0.8218 (tt) cc_final: 0.7993 (mm) REVERT: F 617 TRP cc_start: 0.8310 (t60) cc_final: 0.7898 (t60) REVERT: F 621 TYR cc_start: 0.8625 (t80) cc_final: 0.8278 (t80) REVERT: F 623 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7394 (ttp80) REVERT: F 628 GLU cc_start: 0.8289 (pt0) cc_final: 0.7828 (pt0) REVERT: F 637 PHE cc_start: 0.8261 (m-80) cc_final: 0.8050 (m-80) REVERT: F 672 GLU cc_start: 0.8291 (pp20) cc_final: 0.7870 (pp20) REVERT: F 676 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7814 (ttm-80) outliers start: 49 outliers final: 25 residues processed: 406 average time/residue: 0.0982 time to fit residues: 50.4456 Evaluate side-chains 420 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 383 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 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 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 255 VAL 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 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 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 443 ASN F 313 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN F 502 ASN F 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098741 restraints weight = 15324.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.102501 restraints weight = 7772.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.105047 restraints weight = 4733.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106650 restraints weight = 3253.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107958 restraints weight = 2471.800| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4000 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= 0.145 Angle : 0.717 8.652 9480 Z= 0.355 Chirality : 0.044 0.149 1059 Planarity : 0.006 0.117 1227 Dihedral : 4.853 57.147 936 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.68 % Allowed : 30.97 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.30), residues: 835 helix: 1.31 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 636 TYR 0.025 0.001 TYR F 546 PHE 0.021 0.001 PHE G 503 TRP 0.017 0.002 TRP F 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6996) covalent geometry : angle 0.71710 ( 9476) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.85998 ( 4) hydrogen bonds : bond 0.03936 ( 342) hydrogen bonds : angle 4.50906 ( 984) *********************** 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 441 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 391 time to evaluate : 0.225 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: 0.8516 (mp) cc_final: 0.7896 (pt) REVERT: G 182 SER cc_start: 0.8307 (p) cc_final: 0.7861 (t) REVERT: G 193 GLN cc_start: 0.8724 (mp10) cc_final: 0.8253 (mp10) REVERT: G 201 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8102 (m) REVERT: G 204 ASP cc_start: 0.7693 (t70) cc_final: 0.7330 (t0) REVERT: G 223 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7946 (mtmm) REVERT: G 257 LYS cc_start: 0.8880 (mttt) cc_final: 0.8315 (mttm) REVERT: G 258 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6647 (mtt180) REVERT: G 272 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8583 (mm) REVERT: G 277 MET cc_start: 0.7933 (mmm) cc_final: 0.7648 (mmm) REVERT: G 288 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7246 (tpt170) REVERT: G 290 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7497 (mtp85) REVERT: G 293 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6932 (tm-30) REVERT: G 294 ARG cc_start: 0.6101 (tmt-80) cc_final: 0.5134 (tmt-80) REVERT: G 299 GLN cc_start: 0.8512 (mp10) cc_final: 0.8249 (mp10) REVERT: G 312 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 314 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8231 (pp) REVERT: G 318 LEU cc_start: 0.8890 (tp) cc_final: 0.8492 (tp) REVERT: G 327 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7942 (tm-30) REVERT: G 333 MET cc_start: 0.8470 (ptm) cc_final: 0.7796 (ptp) REVERT: G 342 GLU cc_start: 0.7859 (mp0) cc_final: 0.7335 (mp0) REVERT: G 344 GLU cc_start: 0.8194 (tp30) cc_final: 0.6880 (tp30) REVERT: G 348 ARG cc_start: 0.8513 (mtt180) cc_final: 0.8172 (mmt90) REVERT: G 349 PHE cc_start: 0.8958 (t80) cc_final: 0.8599 (t80) REVERT: G 355 MET cc_start: 0.7845 (tpp) cc_final: 0.6813 (tpp) REVERT: G 359 LEU cc_start: 0.8987 (mt) cc_final: 0.8374 (mm) REVERT: G 408 LYS cc_start: 0.8396 (tppt) cc_final: 0.7985 (tppt) REVERT: G 412 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8071 (ttp-170) REVERT: G 413 ARG cc_start: 0.8544 (mpp80) cc_final: 0.8285 (mpp80) REVERT: G 417 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8366 (mtm-85) REVERT: G 419 CYS cc_start: 0.8596 (m) cc_final: 0.8146 (m) REVERT: G 423 PHE cc_start: 0.8649 (t80) cc_final: 0.8277 (t80) REVERT: G 425 CYS cc_start: 0.8828 (m) cc_final: 0.8495 (m) REVERT: G 426 TYR cc_start: 0.8552 (t80) cc_final: 0.8315 (t80) REVERT: G 429 GLN cc_start: 0.8321 (tt0) cc_final: 0.7995 (tt0) REVERT: G 432 MET cc_start: 0.7841 (mmm) cc_final: 0.7236 (mmm) REVERT: G 443 ASN cc_start: 0.8456 (m-40) cc_final: 0.7541 (m-40) REVERT: G 445 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8292 (mptp) REVERT: G 446 GLU cc_start: 0.7776 (tt0) cc_final: 0.7331 (pt0) REVERT: G 448 GLN cc_start: 0.8397 (mt0) cc_final: 0.7264 (mt0) REVERT: G 449 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7619 (mmmm) REVERT: G 452 LYS cc_start: 0.8644 (mttm) cc_final: 0.7935 (mttm) REVERT: G 453 GLN cc_start: 0.8285 (mt0) cc_final: 0.7880 (mp10) REVERT: G 456 LYS cc_start: 0.9253 (tmtm) cc_final: 0.8842 (tmtm) REVERT: G 458 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8108 (mm) REVERT: G 478 GLU cc_start: 0.8491 (pm20) cc_final: 0.8138 (pm20) REVERT: G 482 LYS cc_start: 0.8489 (tptp) cc_final: 0.7551 (tptp) REVERT: G 483 THR cc_start: 0.8861 (t) cc_final: 0.8578 (p) REVERT: G 486 GLN cc_start: 0.7778 (mm110) cc_final: 0.6737 (mm110) REVERT: G 495 SER cc_start: 0.8745 (m) cc_final: 0.8218 (p) REVERT: G 497 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8556 (mm) REVERT: G 498 GLN cc_start: 0.8685 (tp40) cc_final: 0.8231 (tp40) REVERT: G 501 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.8429 (ttm170) REVERT: G 502 ASN cc_start: 0.8202 (t0) cc_final: 0.7247 (t0) REVERT: G 504 ILE cc_start: 0.8690 (mm) cc_final: 0.8398 (mm) REVERT: G 506 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 507 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8086 (mmm160) REVERT: G 540 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8523 (mm) REVERT: F 167 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5603 (mp) REVERT: F 173 PHE cc_start: 0.7953 (m-80) cc_final: 0.7663 (m-80) REVERT: F 175 GLN cc_start: 0.7201 (tm130) cc_final: 0.6875 (tm-30) REVERT: F 178 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8257 (mmmt) REVERT: F 191 ASP cc_start: 0.8500 (p0) cc_final: 0.7892 (p0) REVERT: F 192 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8008 (mmtt) REVERT: F 193 GLN cc_start: 0.8647 (mm110) cc_final: 0.8303 (mm110) REVERT: F 194 LEU cc_start: 0.8782 (mt) cc_final: 0.8480 (mm) REVERT: F 198 GLN cc_start: 0.8304 (pm20) cc_final: 0.7737 (tp40) REVERT: F 204 ASP cc_start: 0.8231 (p0) cc_final: 0.7974 (p0) REVERT: F 215 PHE cc_start: 0.6703 (m-80) cc_final: 0.6376 (m-80) REVERT: F 271 ASN cc_start: 0.8337 (p0) cc_final: 0.7902 (p0) REVERT: F 277 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7816 (mtt) REVERT: F 316 ARG cc_start: 0.7199 (mmp80) cc_final: 0.6961 (mmp80) REVERT: F 322 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7088 (pm20) REVERT: F 325 ASP cc_start: 0.7951 (m-30) cc_final: 0.7158 (m-30) REVERT: F 333 MET cc_start: 0.7888 (tpp) cc_final: 0.7498 (mpp) REVERT: F 334 MET cc_start: 0.8118 (tpt) cc_final: 0.7771 (tpt) REVERT: F 346 MET cc_start: 0.7710 (mtt) cc_final: 0.6880 (mtt) REVERT: F 349 PHE cc_start: 0.8674 (t80) cc_final: 0.7843 (t80) REVERT: F 355 MET cc_start: 0.8066 (tpp) cc_final: 0.7084 (tpp) REVERT: F 356 GLN cc_start: 0.8554 (tt0) cc_final: 0.7988 (tm-30) REVERT: F 357 ARG cc_start: 0.8500 (ttt180) cc_final: 0.8041 (ttt-90) REVERT: F 358 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8141 (mtpp) REVERT: F 369 GLN cc_start: 0.6795 (tm-30) cc_final: 0.5870 (tm-30) REVERT: F 373 ARG cc_start: 0.8207 (ttt180) cc_final: 0.7748 (ttp80) REVERT: F 383 LEU cc_start: 0.8623 (mm) cc_final: 0.8400 (mt) REVERT: F 394 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: F 405 SER cc_start: 0.8750 (t) cc_final: 0.8532 (p) REVERT: F 419 CYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8308 (p) REVERT: F 423 PHE cc_start: 0.8588 (t80) cc_final: 0.8280 (t80) REVERT: F 434 VAL cc_start: 0.8315 (p) cc_final: 0.8072 (m) REVERT: F 437 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7739 (mm110) REVERT: F 446 GLU cc_start: 0.8384 (tt0) cc_final: 0.7845 (pt0) REVERT: F 448 GLN cc_start: 0.8837 (mt0) cc_final: 0.8289 (mt0) REVERT: F 464 GLU cc_start: 0.7873 (tp30) cc_final: 0.7640 (tp30) REVERT: F 495 SER cc_start: 0.8156 (t) cc_final: 0.7591 (p) REVERT: F 498 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7903 (tp-100) REVERT: F 499 ASN cc_start: 0.8337 (m-40) cc_final: 0.8085 (m-40) REVERT: F 500 PHE cc_start: 0.8002 (t80) cc_final: 0.7794 (t80) REVERT: F 501 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8136 (ttm110) REVERT: F 502 ASN cc_start: 0.7884 (t0) cc_final: 0.7385 (t0) REVERT: F 505 LEU cc_start: 0.8653 (mm) cc_final: 0.8433 (mm) REVERT: F 528 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.5470 (ttp-170) REVERT: F 538 CYS cc_start: 0.8297 (m) cc_final: 0.7719 (m) REVERT: F 539 TYR cc_start: 0.8148 (t80) cc_final: 0.7467 (t80) REVERT: F 575 HIS cc_start: 0.8740 (m90) cc_final: 0.8451 (m90) REVERT: F 576 ARG cc_start: 0.7504 (mmp80) cc_final: 0.7087 (mtm-85) REVERT: F 581 ASN cc_start: 0.8230 (t0) cc_final: 0.7814 (t0) REVERT: F 583 GLN cc_start: 0.8782 (mm110) cc_final: 0.8554 (mm110) REVERT: F 587 GLU cc_start: 0.8225 (tt0) cc_final: 0.7860 (tt0) REVERT: F 611 LYS cc_start: 0.8536 (pttt) cc_final: 0.8319 (pttt) REVERT: F 616 LEU cc_start: 0.8204 (tt) cc_final: 0.7939 (mm) REVERT: F 617 TRP cc_start: 0.8270 (t60) cc_final: 0.7862 (t60) REVERT: F 621 TYR cc_start: 0.8619 (t80) cc_final: 0.8278 (t80) REVERT: F 623 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7435 (ttp80) REVERT: F 628 GLU cc_start: 0.8287 (pt0) cc_final: 0.7848 (pt0) REVERT: F 672 GLU cc_start: 0.8241 (pp20) cc_final: 0.7828 (pp20) REVERT: F 676 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7798 (ttm-80) outliers start: 50 outliers final: 35 residues processed: 404 average time/residue: 0.1023 time to fit residues: 52.0281 Evaluate side-chains 429 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 380 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 447 LEU Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU 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 167 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 207 SER 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 340 THR 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 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 613 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 659 ILE Chi-restraints excluded: chain F residue 664 GLN 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 30 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.117274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098723 restraints weight = 15307.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102520 restraints weight = 7772.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105066 restraints weight = 4741.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106850 restraints weight = 3264.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.107987 restraints weight = 2450.856| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4190 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= 0.131 Angle : 0.728 15.557 9480 Z= 0.354 Chirality : 0.044 0.163 1059 Planarity : 0.004 0.055 1227 Dihedral : 4.782 57.847 936 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.41 % Allowed : 32.44 % Favored : 61.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.30), residues: 835 helix: 1.39 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 252 TYR 0.026 0.002 TYR F 546 PHE 0.013 0.001 PHE F 174 TRP 0.017 0.002 TRP F 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6996) covalent geometry : angle 0.72756 ( 9476) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.82203 ( 4) hydrogen bonds : bond 0.03826 ( 342) hydrogen bonds : angle 4.45937 ( 984) *********************** 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 430 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.315 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: 0.8501 (mp) cc_final: 0.7871 (pt) REVERT: G 182 SER cc_start: 0.8293 (p) cc_final: 0.7836 (t) REVERT: G 193 GLN cc_start: 0.8734 (mp10) cc_final: 0.8240 (mp10) REVERT: G 201 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8044 (m) REVERT: G 204 ASP cc_start: 0.7679 (t70) cc_final: 0.7294 (t0) REVERT: G 223 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7944 (mtmm) REVERT: G 252 ARG cc_start: 0.8259 (ttt-90) cc_final: 0.7961 (ttt-90) REVERT: G 257 LYS cc_start: 0.8856 (mttt) cc_final: 0.8311 (mttm) REVERT: G 258 ARG cc_start: 0.6928 (mtt180) cc_final: 0.6396 (mtt180) REVERT: G 272 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8579 (mm) REVERT: G 277 MET cc_start: 0.7930 (mmm) cc_final: 0.7643 (mmm) REVERT: G 288 ARG cc_start: 0.7997 (tpp-160) cc_final: 0.7236 (tpt170) REVERT: G 290 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7498 (mtp85) REVERT: G 293 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6971 (tm-30) REVERT: G 294 ARG cc_start: 0.6199 (tmt-80) cc_final: 0.5293 (tmt170) REVERT: G 312 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7765 (tm-30) REVERT: G 314 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8224 (pp) REVERT: G 318 LEU cc_start: 0.8873 (tp) cc_final: 0.8463 (tp) REVERT: G 327 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7961 (tm-30) REVERT: G 333 MET cc_start: 0.8497 (ptm) cc_final: 0.7502 (ptp) REVERT: G 342 GLU cc_start: 0.7888 (mp0) cc_final: 0.7306 (mp0) REVERT: G 344 GLU cc_start: 0.8176 (tp30) cc_final: 0.6411 (tp30) REVERT: G 347 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8127 (tm-30) REVERT: G 348 ARG cc_start: 0.8480 (mtt180) cc_final: 0.8127 (mmt90) REVERT: G 349 PHE cc_start: 0.8927 (t80) cc_final: 0.8597 (t80) REVERT: G 355 MET cc_start: 0.7870 (tpp) cc_final: 0.6835 (tpp) REVERT: G 359 LEU cc_start: 0.8976 (mt) cc_final: 0.8388 (mm) REVERT: G 408 LYS cc_start: 0.8346 (tppt) cc_final: 0.8013 (tppt) REVERT: G 412 ARG cc_start: 0.8512 (ttt180) cc_final: 0.7965 (ptm-80) REVERT: G 413 ARG cc_start: 0.8536 (mpp80) cc_final: 0.8285 (mpp80) REVERT: G 417 ARG cc_start: 0.8741 (mtm110) cc_final: 0.8377 (mtm-85) REVERT: G 419 CYS cc_start: 0.8580 (m) cc_final: 0.8011 (m) REVERT: G 423 PHE cc_start: 0.8642 (t80) cc_final: 0.8278 (t80) REVERT: G 425 CYS cc_start: 0.8802 (m) cc_final: 0.8474 (m) REVERT: G 426 TYR cc_start: 0.8546 (t80) cc_final: 0.8336 (t80) REVERT: G 429 GLN cc_start: 0.8367 (tt0) cc_final: 0.7994 (tt0) REVERT: G 432 MET cc_start: 0.7903 (mmm) cc_final: 0.7527 (mmm) REVERT: G 437 GLN cc_start: 0.8298 (tm-30) cc_final: 0.8090 (tm-30) REVERT: G 443 ASN cc_start: 0.8359 (m-40) cc_final: 0.7553 (m110) REVERT: G 445 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (mptp) REVERT: G 446 GLU cc_start: 0.7681 (tt0) cc_final: 0.7276 (pt0) REVERT: G 448 GLN cc_start: 0.8379 (mt0) cc_final: 0.7236 (mt0) REVERT: G 449 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7568 (mmmm) REVERT: G 452 LYS cc_start: 0.8613 (mttm) cc_final: 0.7898 (mttm) REVERT: G 453 GLN cc_start: 0.8293 (mt0) cc_final: 0.7879 (mp10) REVERT: G 456 LYS cc_start: 0.9254 (tmtm) cc_final: 0.8851 (tmtm) REVERT: G 478 GLU cc_start: 0.8491 (pm20) cc_final: 0.8153 (pm20) REVERT: G 482 LYS cc_start: 0.8447 (tptp) cc_final: 0.7427 (tptp) REVERT: G 483 THR cc_start: 0.8871 (t) cc_final: 0.8594 (p) REVERT: G 486 GLN cc_start: 0.7793 (mm110) cc_final: 0.6676 (mm110) REVERT: G 495 SER cc_start: 0.8743 (m) cc_final: 0.8223 (p) REVERT: G 497 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8541 (mm) REVERT: G 498 GLN cc_start: 0.8660 (tp40) cc_final: 0.7626 (tp40) REVERT: G 501 ARG cc_start: 0.8666 (ttp-170) cc_final: 0.8017 (ptp-110) REVERT: G 502 ASN cc_start: 0.8191 (t0) cc_final: 0.7226 (t0) REVERT: G 504 ILE cc_start: 0.8690 (mm) cc_final: 0.8412 (mm) REVERT: G 506 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7449 (mm-30) REVERT: G 507 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8085 (mmm160) REVERT: G 540 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8489 (mm) REVERT: F 173 PHE cc_start: 0.7940 (m-80) cc_final: 0.7634 (m-80) REVERT: F 175 GLN cc_start: 0.7238 (tm130) cc_final: 0.6863 (tm-30) REVERT: F 178 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8262 (mmmt) REVERT: F 191 ASP cc_start: 0.8459 (p0) cc_final: 0.7790 (p0) REVERT: F 192 LYS cc_start: 0.8732 (mmtt) cc_final: 0.7958 (mmtt) REVERT: F 193 GLN cc_start: 0.8645 (mm110) cc_final: 0.8300 (mm110) REVERT: F 194 LEU cc_start: 0.8755 (mt) cc_final: 0.8477 (mm) REVERT: F 198 GLN cc_start: 0.8300 (pm20) cc_final: 0.7702 (tp40) REVERT: F 204 ASP cc_start: 0.8245 (p0) cc_final: 0.7995 (p0) REVERT: F 215 PHE cc_start: 0.6696 (m-80) cc_final: 0.6390 (m-80) REVERT: F 253 LEU cc_start: 0.9038 (mm) cc_final: 0.8783 (mt) REVERT: F 271 ASN cc_start: 0.8406 (p0) cc_final: 0.7876 (p0) REVERT: F 277 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: F 284 LEU cc_start: 0.6822 (mt) cc_final: 0.6105 (tt) REVERT: F 325 ASP cc_start: 0.7917 (m-30) cc_final: 0.7451 (m-30) REVERT: F 333 MET cc_start: 0.7869 (tpp) cc_final: 0.7540 (mpp) REVERT: F 334 MET cc_start: 0.8109 (tpt) cc_final: 0.7733 (tpt) REVERT: F 342 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7937 (mm-30) REVERT: F 346 MET cc_start: 0.7680 (mtt) cc_final: 0.6869 (mtt) REVERT: F 349 PHE cc_start: 0.8689 (t80) cc_final: 0.7862 (t80) REVERT: F 355 MET cc_start: 0.8029 (tpp) cc_final: 0.7016 (tpp) REVERT: F 356 GLN cc_start: 0.8546 (tt0) cc_final: 0.8084 (tt0) REVERT: F 357 ARG cc_start: 0.8492 (ttt180) cc_final: 0.8028 (ttt-90) REVERT: F 358 LYS cc_start: 0.8647 (mtpp) cc_final: 0.7881 (mtpp) REVERT: F 362 THR cc_start: 0.8764 (t) cc_final: 0.8455 (p) REVERT: F 365 TYR cc_start: 0.8107 (m-80) cc_final: 0.7890 (m-80) REVERT: F 369 GLN cc_start: 0.6796 (tm-30) cc_final: 0.5893 (tm-30) REVERT: F 373 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7714 (ttp80) REVERT: F 383 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8307 (mt) REVERT: F 394 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.6998 (t-90) REVERT: F 405 SER cc_start: 0.8705 (t) cc_final: 0.8486 (p) REVERT: F 419 CYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8324 (p) REVERT: F 423 PHE cc_start: 0.8581 (t80) cc_final: 0.8223 (t80) REVERT: F 434 VAL cc_start: 0.8314 (p) cc_final: 0.8076 (m) REVERT: F 435 TRP cc_start: 0.8088 (t60) cc_final: 0.7879 (t60) REVERT: F 437 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7719 (mm110) REVERT: F 446 GLU cc_start: 0.8383 (tt0) cc_final: 0.7851 (pt0) REVERT: F 448 GLN cc_start: 0.8835 (mt0) cc_final: 0.8299 (mt0) REVERT: F 464 GLU cc_start: 0.7963 (tp30) cc_final: 0.7559 (tp30) REVERT: F 485 GLN cc_start: 0.7649 (mt0) cc_final: 0.7081 (mt0) REVERT: F 495 SER cc_start: 0.8137 (t) cc_final: 0.7542 (p) REVERT: F 498 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7499 (tp-100) REVERT: F 499 ASN cc_start: 0.8335 (m-40) cc_final: 0.8064 (m-40) REVERT: F 501 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7950 (ptm160) REVERT: F 502 ASN cc_start: 0.7891 (t0) cc_final: 0.7390 (t0) REVERT: F 503 PHE cc_start: 0.8608 (t80) cc_final: 0.8376 (t80) REVERT: F 528 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6149 (mtm180) REVERT: F 539 TYR cc_start: 0.8132 (t80) cc_final: 0.7463 (t80) REVERT: F 541 LEU cc_start: 0.8743 (tp) cc_final: 0.8487 (tt) REVERT: F 575 HIS cc_start: 0.8717 (m90) cc_final: 0.8149 (m90) REVERT: F 576 ARG cc_start: 0.7508 (mmp80) cc_final: 0.7085 (mtm-85) REVERT: F 581 ASN cc_start: 0.8232 (t0) cc_final: 0.7801 (t0) REVERT: F 583 GLN cc_start: 0.8775 (mm110) cc_final: 0.8547 (mm110) REVERT: F 587 GLU cc_start: 0.8217 (tt0) cc_final: 0.7868 (tt0) REVERT: F 611 LYS cc_start: 0.8473 (pttt) cc_final: 0.8266 (pttt) REVERT: F 616 LEU cc_start: 0.8202 (tt) cc_final: 0.7938 (mm) REVERT: F 617 TRP cc_start: 0.8286 (t60) cc_final: 0.7905 (t60) REVERT: F 621 TYR cc_start: 0.8624 (t80) cc_final: 0.8330 (t80) REVERT: F 622 LEU cc_start: 0.8696 (mm) cc_final: 0.8465 (mt) REVERT: F 623 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7393 (ttp80) REVERT: F 628 GLU cc_start: 0.8286 (pt0) cc_final: 0.7850 (pt0) REVERT: F 672 GLU cc_start: 0.8267 (pp20) cc_final: 0.7777 (pp20) REVERT: F 676 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7803 (ttm-80) outliers start: 48 outliers final: 29 residues processed: 395 average time/residue: 0.1056 time to fit residues: 52.4961 Evaluate side-chains 417 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 464 GLU 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 179 ILE 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 257 LYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 383 LEU 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 481 LEU Chi-restraints excluded: chain F residue 507 ARG 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 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 9 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 53 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: ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 GLN ** F 686 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 = 0.3735 r_free = 0.3735 target = 0.116806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098330 restraints weight = 15112.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102048 restraints weight = 7713.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104627 restraints weight = 4748.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.106392 restraints weight = 3249.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107567 restraints weight = 2440.500| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6998 Z= 0.145 Angle : 0.776 13.575 9480 Z= 0.372 Chirality : 0.046 0.234 1059 Planarity : 0.004 0.048 1227 Dihedral : 4.885 59.988 936 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.54 % Allowed : 32.04 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.30), residues: 835 helix: 1.45 (0.25), residues: 473 sheet: -0.50 (1.90), residues: 12 loop : -1.22 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 252 TYR 0.029 0.002 TYR F 546 PHE 0.023 0.001 PHE G 503 TRP 0.020 0.002 TRP G 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6996) covalent geometry : angle 0.77618 ( 9476) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.60166 ( 4) hydrogen bonds : bond 0.03838 ( 342) hydrogen bonds : angle 4.48125 ( 984) *********************** 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 437 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 388 time to evaluate : 0.284 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 182 SER cc_start: 0.8286 (p) cc_final: 0.7579 (t) REVERT: G 192 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8600 (mtmt) REVERT: G 193 GLN cc_start: 0.8730 (mp10) cc_final: 0.8213 (mp10) REVERT: G 201 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8069 (m) REVERT: G 204 ASP cc_start: 0.7694 (t70) cc_final: 0.7317 (t0) REVERT: G 223 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7943 (mtmm) REVERT: G 258 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6395 (mtt180) REVERT: G 272 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8571 (mm) REVERT: G 277 MET cc_start: 0.7943 (mmm) cc_final: 0.7649 (mmm) REVERT: G 283 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6708 (mm-30) REVERT: G 288 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7278 (tpt170) REVERT: G 290 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7527 (mtp85) REVERT: G 293 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6948 (tm-30) REVERT: G 294 ARG cc_start: 0.5780 (tmt-80) cc_final: 0.4633 (tmt170) REVERT: G 312 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7679 (tm-30) REVERT: G 314 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (pp) REVERT: G 318 LEU cc_start: 0.8879 (tp) cc_final: 0.8485 (tp) REVERT: G 327 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 333 MET cc_start: 0.8541 (ptm) cc_final: 0.7836 (ptp) REVERT: G 342 GLU cc_start: 0.7877 (mp0) cc_final: 0.7340 (mp0) REVERT: G 344 GLU cc_start: 0.8166 (tp30) cc_final: 0.6939 (tp30) REVERT: G 349 PHE cc_start: 0.8949 (t80) cc_final: 0.8633 (t80) REVERT: G 355 MET cc_start: 0.7947 (tpp) cc_final: 0.6929 (tpp) REVERT: G 359 LEU cc_start: 0.8967 (mt) cc_final: 0.8396 (mm) REVERT: G 413 ARG cc_start: 0.8497 (mpp80) cc_final: 0.8280 (mpp80) REVERT: G 417 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8389 (mtm-85) REVERT: G 418 ASP cc_start: 0.8375 (t70) cc_final: 0.8158 (t70) REVERT: G 419 CYS cc_start: 0.8714 (m) cc_final: 0.8130 (m) REVERT: G 422 LEU cc_start: 0.8776 (mt) cc_final: 0.8306 (mp) REVERT: G 423 PHE cc_start: 0.8657 (t80) cc_final: 0.8232 (t80) REVERT: G 425 CYS cc_start: 0.8826 (m) cc_final: 0.8515 (m) REVERT: G 426 TYR cc_start: 0.8625 (t80) cc_final: 0.8400 (t80) REVERT: G 429 GLN cc_start: 0.8403 (tt0) cc_final: 0.8031 (tt0) REVERT: G 432 MET cc_start: 0.7846 (mmm) cc_final: 0.7465 (mmm) REVERT: G 437 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8101 (tm-30) REVERT: G 445 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8359 (mptp) REVERT: G 448 GLN cc_start: 0.8357 (mt0) cc_final: 0.7466 (mt0) REVERT: G 449 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7620 (mmmm) REVERT: G 452 LYS cc_start: 0.8656 (mttm) cc_final: 0.8055 (mttm) REVERT: G 453 GLN cc_start: 0.8359 (mt0) cc_final: 0.7992 (mp10) REVERT: G 456 LYS cc_start: 0.9274 (tmtm) cc_final: 0.8831 (tmtm) REVERT: G 459 TRP cc_start: 0.8413 (m100) cc_final: 0.8144 (m100) REVERT: G 478 GLU cc_start: 0.8532 (pm20) cc_final: 0.8185 (pm20) REVERT: G 482 LYS cc_start: 0.8471 (tptp) cc_final: 0.7394 (tptp) REVERT: G 483 THR cc_start: 0.8856 (t) cc_final: 0.8590 (p) REVERT: G 486 GLN cc_start: 0.7819 (mm110) cc_final: 0.6705 (mm110) REVERT: G 495 SER cc_start: 0.8731 (m) cc_final: 0.8213 (p) REVERT: G 497 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (mm) REVERT: G 498 GLN cc_start: 0.8665 (tp40) cc_final: 0.7637 (tp40) REVERT: G 501 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8088 (ptp-110) REVERT: G 502 ASN cc_start: 0.8201 (t0) cc_final: 0.7273 (t0) REVERT: G 504 ILE cc_start: 0.8698 (mm) cc_final: 0.8436 (mm) REVERT: G 506 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7496 (mm-30) REVERT: G 507 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8110 (mmm160) REVERT: G 518 LEU cc_start: 0.8485 (pp) cc_final: 0.8284 (pp) REVERT: G 540 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8524 (mm) REVERT: F 167 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5941 (pt) REVERT: F 173 PHE cc_start: 0.7932 (m-80) cc_final: 0.7606 (m-80) REVERT: F 175 GLN cc_start: 0.7325 (tm130) cc_final: 0.6887 (tm-30) REVERT: F 178 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8259 (mmmt) REVERT: F 191 ASP cc_start: 0.8436 (p0) cc_final: 0.7816 (p0) REVERT: F 192 LYS cc_start: 0.8695 (mmtt) cc_final: 0.7943 (mmtt) REVERT: F 193 GLN cc_start: 0.8662 (mm110) cc_final: 0.8329 (mm110) REVERT: F 194 LEU cc_start: 0.8765 (mt) cc_final: 0.8489 (mm) REVERT: F 198 GLN cc_start: 0.8289 (pm20) cc_final: 0.7669 (tp40) REVERT: F 204 ASP cc_start: 0.8272 (p0) cc_final: 0.7974 (p0) REVERT: F 215 PHE cc_start: 0.6717 (m-80) cc_final: 0.6357 (m-80) REVERT: F 253 LEU cc_start: 0.9046 (mm) cc_final: 0.8783 (mt) REVERT: F 271 ASN cc_start: 0.8503 (p0) cc_final: 0.8000 (p0) REVERT: F 277 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7940 (mtt) REVERT: F 325 ASP cc_start: 0.7998 (m-30) cc_final: 0.7587 (m-30) REVERT: F 327 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7761 (mm-30) REVERT: F 330 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7839 (ptt90) REVERT: F 333 MET cc_start: 0.7887 (tpp) cc_final: 0.7525 (mpp) REVERT: F 334 MET cc_start: 0.8190 (tpt) cc_final: 0.7854 (tpt) REVERT: F 342 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8028 (mm-30) REVERT: F 346 MET cc_start: 0.7709 (mtt) cc_final: 0.6945 (mtt) REVERT: F 347 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7663 (tp40) REVERT: F 349 PHE cc_start: 0.8728 (t80) cc_final: 0.7874 (t80) REVERT: F 355 MET cc_start: 0.8048 (tpp) cc_final: 0.6991 (tpp) REVERT: F 356 GLN cc_start: 0.8579 (tt0) cc_final: 0.8090 (tt0) REVERT: F 357 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8046 (ttt-90) REVERT: F 358 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8103 (mtpp) REVERT: F 365 TYR cc_start: 0.8138 (m-80) cc_final: 0.7904 (m-80) REVERT: F 369 GLN cc_start: 0.6770 (tm-30) cc_final: 0.5849 (tm-30) REVERT: F 373 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7715 (ttp80) REVERT: F 383 LEU cc_start: 0.8532 (mm) cc_final: 0.8320 (mt) REVERT: F 394 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: F 405 SER cc_start: 0.8730 (t) cc_final: 0.8525 (p) REVERT: F 419 CYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8342 (p) REVERT: F 427 THR cc_start: 0.8840 (p) cc_final: 0.8559 (t) REVERT: F 434 VAL cc_start: 0.8327 (p) cc_final: 0.8087 (m) REVERT: F 437 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7734 (mm110) REVERT: F 446 GLU cc_start: 0.8391 (tt0) cc_final: 0.7867 (pt0) REVERT: F 448 GLN cc_start: 0.8806 (mt0) cc_final: 0.8294 (mt0) REVERT: F 464 GLU cc_start: 0.8049 (tp30) cc_final: 0.7578 (tp30) REVERT: F 485 GLN cc_start: 0.7764 (mt0) cc_final: 0.7233 (mt0) REVERT: F 495 SER cc_start: 0.8293 (t) cc_final: 0.7744 (p) REVERT: F 498 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7885 (tp-100) REVERT: F 499 ASN cc_start: 0.8337 (m-40) cc_final: 0.8087 (m-40) REVERT: F 501 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8144 (ttm110) REVERT: F 502 ASN cc_start: 0.7884 (t0) cc_final: 0.7387 (t0) REVERT: F 505 LEU cc_start: 0.8614 (mm) cc_final: 0.8399 (mm) REVERT: F 526 LYS cc_start: 0.5232 (ptpt) cc_final: 0.4387 (ptmt) REVERT: F 528 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.4959 (ttp80) REVERT: F 539 TYR cc_start: 0.8175 (t80) cc_final: 0.7452 (t80) REVERT: F 541 LEU cc_start: 0.8695 (tp) cc_final: 0.8416 (tt) REVERT: F 576 ARG cc_start: 0.7500 (mmp80) cc_final: 0.6962 (mtm-85) REVERT: F 581 ASN cc_start: 0.8253 (t0) cc_final: 0.7822 (t0) REVERT: F 583 GLN cc_start: 0.8778 (mm110) cc_final: 0.8549 (mm110) REVERT: F 587 GLU cc_start: 0.8277 (tt0) cc_final: 0.7918 (tt0) REVERT: F 611 LYS cc_start: 0.8501 (pttt) cc_final: 0.8072 (mmtm) REVERT: F 616 LEU cc_start: 0.8188 (tt) cc_final: 0.7959 (mm) REVERT: F 617 TRP cc_start: 0.8234 (t60) cc_final: 0.7876 (t60) REVERT: F 621 TYR cc_start: 0.8580 (t80) cc_final: 0.8183 (t80) REVERT: F 622 LEU cc_start: 0.8814 (mm) cc_final: 0.8432 (mt) REVERT: F 623 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7421 (ttp80) REVERT: F 628 GLU cc_start: 0.8286 (pt0) cc_final: 0.7549 (pt0) REVERT: F 646 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7930 (t0) REVERT: F 672 GLU cc_start: 0.8279 (pp20) cc_final: 0.7780 (pp20) REVERT: F 676 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7821 (ttm-80) outliers start: 49 outliers final: 27 residues processed: 402 average time/residue: 0.1089 time to fit residues: 54.9827 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 : 0.267 ------------------------------------------------------------------------------- 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 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 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 464 GLU 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 179 ILE 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 277 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 10.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 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 = 0.3730 r_free = 0.3730 target = 0.116307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097610 restraints weight = 15300.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101382 restraints weight = 7789.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103943 restraints weight = 4775.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105622 restraints weight = 3312.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106867 restraints weight = 2518.163| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4589 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= 0.144 Angle : 0.784 12.954 9480 Z= 0.375 Chirality : 0.045 0.213 1059 Planarity : 0.005 0.065 1227 Dihedral : 4.878 57.073 936 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.30), residues: 835 helix: 1.46 (0.24), residues: 474 sheet: -0.59 (1.87), residues: 12 loop : -1.26 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 252 TYR 0.030 0.001 TYR F 546 PHE 0.022 0.001 PHE F 423 TRP 0.023 0.002 TRP F 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6996) covalent geometry : angle 0.78378 ( 9476) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.70576 ( 4) hydrogen bonds : bond 0.03831 ( 342) hydrogen bonds : angle 4.45567 ( 984) *********************** 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 429 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 384 time to evaluate : 0.266 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 174 PHE cc_start: 0.7241 (m-10) cc_final: 0.6959 (m-10) REVERT: G 182 SER cc_start: 0.8276 (p) cc_final: 0.7567 (t) REVERT: G 192 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8594 (mtmt) REVERT: G 193 GLN cc_start: 0.8678 (mp10) cc_final: 0.8206 (mp10) REVERT: G 201 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8025 (m) REVERT: G 204 ASP cc_start: 0.7699 (t70) cc_final: 0.7323 (t0) REVERT: G 223 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7952 (mtmm) REVERT: G 258 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6398 (mtt180) REVERT: G 272 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8598 (mm) REVERT: G 277 MET cc_start: 0.7967 (mmm) cc_final: 0.7681 (mmm) REVERT: G 283 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6706 (mm-30) REVERT: G 288 ARG cc_start: 0.8055 (tpp-160) cc_final: 0.7221 (tpt170) REVERT: G 290 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7544 (mtp85) REVERT: G 293 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6944 (tm-30) REVERT: G 294 ARG cc_start: 0.5834 (tmt-80) cc_final: 0.4679 (tmt-80) REVERT: G 312 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7681 (tm-30) REVERT: G 314 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8249 (pp) REVERT: G 318 LEU cc_start: 0.8879 (tp) cc_final: 0.8513 (tp) REVERT: G 327 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8032 (tm-30) REVERT: G 333 MET cc_start: 0.8471 (ptm) cc_final: 0.7699 (ptp) REVERT: G 342 GLU cc_start: 0.7889 (mp0) cc_final: 0.7342 (mp0) REVERT: G 344 GLU cc_start: 0.8166 (tp30) cc_final: 0.6623 (tp30) REVERT: G 347 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 349 PHE cc_start: 0.8914 (t80) cc_final: 0.8581 (t80) REVERT: G 355 MET cc_start: 0.7972 (tpp) cc_final: 0.7033 (tpp) REVERT: G 359 LEU cc_start: 0.8968 (mt) cc_final: 0.8478 (mm) REVERT: G 412 ARG cc_start: 0.8519 (ttt180) cc_final: 0.7969 (ptm-80) REVERT: G 417 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8397 (mtm-85) REVERT: G 418 ASP cc_start: 0.8365 (t70) cc_final: 0.7923 (t70) REVERT: G 419 CYS cc_start: 0.8711 (m) cc_final: 0.8111 (m) REVERT: G 422 LEU cc_start: 0.8823 (mt) cc_final: 0.8339 (mp) REVERT: G 423 PHE cc_start: 0.8654 (t80) cc_final: 0.8186 (t80) REVERT: G 425 CYS cc_start: 0.8872 (m) cc_final: 0.8547 (m) REVERT: G 426 TYR cc_start: 0.8652 (t80) cc_final: 0.8413 (t80) REVERT: G 429 GLN cc_start: 0.8396 (tt0) cc_final: 0.8013 (tt0) REVERT: G 432 MET cc_start: 0.7852 (mmm) cc_final: 0.7482 (mmm) REVERT: G 437 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8125 (tm-30) REVERT: G 442 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.7336 (mtp-110) REVERT: G 443 ASN cc_start: 0.8214 (m-40) cc_final: 0.7927 (m-40) REVERT: G 445 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8362 (mptp) REVERT: G 448 GLN cc_start: 0.8378 (mt0) cc_final: 0.7492 (mt0) REVERT: G 449 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7642 (mmmm) REVERT: G 452 LYS cc_start: 0.8635 (mttm) cc_final: 0.8071 (mttm) REVERT: G 453 GLN cc_start: 0.8380 (mt0) cc_final: 0.8003 (mp10) REVERT: G 456 LYS cc_start: 0.9263 (tmtm) cc_final: 0.8822 (tmtm) REVERT: G 459 TRP cc_start: 0.8418 (m100) cc_final: 0.8189 (m100) REVERT: G 478 GLU cc_start: 0.8539 (pm20) cc_final: 0.8202 (pm20) REVERT: G 482 LYS cc_start: 0.8481 (tptp) cc_final: 0.7389 (tptp) REVERT: G 483 THR cc_start: 0.8854 (t) cc_final: 0.8586 (p) REVERT: G 486 GLN cc_start: 0.7821 (mm110) cc_final: 0.6762 (mm110) REVERT: G 490 ASP cc_start: 0.7819 (p0) cc_final: 0.7590 (p0) REVERT: G 495 SER cc_start: 0.8723 (m) cc_final: 0.8228 (p) REVERT: G 497 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8522 (mm) REVERT: G 498 GLN cc_start: 0.8660 (tp40) cc_final: 0.7638 (tp40) REVERT: G 501 ARG cc_start: 0.8698 (ttp-170) cc_final: 0.8076 (ptp-110) REVERT: G 502 ASN cc_start: 0.8177 (t0) cc_final: 0.7323 (t0) REVERT: G 504 ILE cc_start: 0.8693 (mm) cc_final: 0.8345 (mm) REVERT: G 506 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7574 (mm-30) REVERT: G 507 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8075 (mmm160) REVERT: G 518 LEU cc_start: 0.8309 (pp) cc_final: 0.8062 (pp) REVERT: G 540 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (mm) REVERT: F 167 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5951 (pt) REVERT: F 173 PHE cc_start: 0.7923 (m-80) cc_final: 0.7644 (m-80) REVERT: F 175 GLN cc_start: 0.7358 (tm130) cc_final: 0.6698 (tm-30) REVERT: F 178 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8270 (mmmt) REVERT: F 191 ASP cc_start: 0.8436 (p0) cc_final: 0.8168 (p0) REVERT: F 192 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8003 (mmtt) REVERT: F 193 GLN cc_start: 0.8659 (mm110) cc_final: 0.8316 (mm110) REVERT: F 194 LEU cc_start: 0.8761 (mt) cc_final: 0.8443 (mm) REVERT: F 198 GLN cc_start: 0.8287 (pm20) cc_final: 0.7802 (tp40) REVERT: F 204 ASP cc_start: 0.8287 (p0) cc_final: 0.8025 (p0) REVERT: F 215 PHE cc_start: 0.6715 (m-80) cc_final: 0.6416 (m-80) REVERT: F 253 LEU cc_start: 0.9058 (mm) cc_final: 0.8788 (mt) REVERT: F 271 ASN cc_start: 0.8538 (p0) cc_final: 0.8140 (p0) REVERT: F 277 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: F 284 LEU cc_start: 0.6827 (mt) cc_final: 0.6122 (tt) REVERT: F 325 ASP cc_start: 0.8023 (m-30) cc_final: 0.7678 (m-30) REVERT: F 327 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7643 (mm-30) REVERT: F 333 MET cc_start: 0.7845 (tpp) cc_final: 0.7541 (mpp) REVERT: F 334 MET cc_start: 0.8199 (tpt) cc_final: 0.7852 (tpt) REVERT: F 346 MET cc_start: 0.7731 (mtt) cc_final: 0.7026 (mtt) REVERT: F 349 PHE cc_start: 0.8713 (t80) cc_final: 0.7859 (t80) REVERT: F 355 MET cc_start: 0.8046 (tpp) cc_final: 0.6747 (tpp) REVERT: F 356 GLN cc_start: 0.8589 (tt0) cc_final: 0.8142 (tm-30) REVERT: F 357 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8048 (ttt-90) REVERT: F 358 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8092 (mtpp) REVERT: F 359 LEU cc_start: 0.9074 (mm) cc_final: 0.8360 (mm) REVERT: F 360 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8322 (mt-10) REVERT: F 365 TYR cc_start: 0.8171 (m-80) cc_final: 0.7888 (m-80) REVERT: F 369 GLN cc_start: 0.6770 (tm-30) cc_final: 0.5891 (tm-30) REVERT: F 373 ARG cc_start: 0.8196 (ttt180) cc_final: 0.7740 (ttp80) REVERT: F 383 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8320 (mt) REVERT: F 394 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: F 405 SER cc_start: 0.8726 (t) cc_final: 0.8516 (p) REVERT: F 419 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8409 (p) REVERT: F 427 THR cc_start: 0.8858 (p) cc_final: 0.8591 (t) REVERT: F 434 VAL cc_start: 0.8331 (p) cc_final: 0.8092 (m) REVERT: F 437 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7748 (mm110) REVERT: F 446 GLU cc_start: 0.8395 (tt0) cc_final: 0.7872 (pt0) REVERT: F 448 GLN cc_start: 0.8804 (mt0) cc_final: 0.8278 (mt0) REVERT: F 464 GLU cc_start: 0.7998 (tp30) cc_final: 0.7468 (tp30) REVERT: F 485 GLN cc_start: 0.7768 (mt0) cc_final: 0.7200 (mt0) REVERT: F 495 SER cc_start: 0.8315 (t) cc_final: 0.7790 (p) REVERT: F 498 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7920 (tp-100) REVERT: F 499 ASN cc_start: 0.8339 (m-40) cc_final: 0.8070 (m-40) REVERT: F 501 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8265 (ttm110) REVERT: F 502 ASN cc_start: 0.7876 (t0) cc_final: 0.7399 (t0) REVERT: F 528 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6318 (ptp-170) REVERT: F 534 LEU cc_start: 0.8757 (mt) cc_final: 0.8551 (mm) REVERT: F 539 TYR cc_start: 0.8160 (t80) cc_final: 0.7525 (t80) REVERT: F 576 ARG cc_start: 0.7516 (mmp80) cc_final: 0.7051 (mtm-85) REVERT: F 581 ASN cc_start: 0.8252 (t0) cc_final: 0.7814 (t0) REVERT: F 583 GLN cc_start: 0.8777 (mm110) cc_final: 0.8558 (mm110) REVERT: F 587 GLU cc_start: 0.8421 (tt0) cc_final: 0.8114 (tt0) REVERT: F 611 LYS cc_start: 0.8532 (pttt) cc_final: 0.8117 (mmtm) REVERT: F 616 LEU cc_start: 0.8182 (tt) cc_final: 0.7959 (mm) REVERT: F 617 TRP cc_start: 0.8217 (t60) cc_final: 0.7837 (t60) REVERT: F 621 TYR cc_start: 0.8613 (t80) cc_final: 0.8267 (t80) REVERT: F 622 LEU cc_start: 0.8829 (mm) cc_final: 0.8471 (mt) REVERT: F 623 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7379 (ttp80) REVERT: F 628 GLU cc_start: 0.8286 (pt0) cc_final: 0.7572 (pt0) REVERT: F 646 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7957 (t0) REVERT: F 676 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7823 (ttm-80) outliers start: 45 outliers final: 26 residues processed: 398 average time/residue: 0.1080 time to fit residues: 53.9273 Evaluate side-chains 419 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 439 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 449 LYS 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 179 ILE 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 383 LEU 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 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 507 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097833 restraints weight = 15225.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101606 restraints weight = 7809.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104150 restraints weight = 4810.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105904 restraints weight = 3337.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107168 restraints weight = 2530.283| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6998 Z= 0.140 Angle : 0.793 12.593 9480 Z= 0.382 Chirality : 0.045 0.210 1059 Planarity : 0.005 0.077 1227 Dihedral : 4.853 55.013 936 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.07 % Allowed : 33.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.30), residues: 835 helix: 1.43 (0.25), residues: 473 sheet: -0.59 (1.87), residues: 12 loop : -1.29 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 316 TYR 0.029 0.001 TYR F 546 PHE 0.022 0.001 PHE G 503 TRP 0.018 0.002 TRP F 435 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6996) covalent geometry : angle 0.79254 ( 9476) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.71095 ( 4) hydrogen bonds : bond 0.03876 ( 342) hydrogen bonds : angle 4.47453 ( 984) *********************** 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 423 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 385 time to evaluate : 0.277 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: 0.7229 (m-10) cc_final: 0.6956 (m-10) REVERT: G 182 SER cc_start: 0.8273 (p) cc_final: 0.7554 (t) REVERT: G 192 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8548 (mtmt) REVERT: G 193 GLN cc_start: 0.8677 (mp10) cc_final: 0.8465 (mp10) REVERT: G 201 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8042 (m) REVERT: G 204 ASP cc_start: 0.7704 (t70) cc_final: 0.7327 (t0) REVERT: G 223 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7963 (mtmm) REVERT: G 258 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6581 (mtt180) REVERT: G 272 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8590 (mm) REVERT: G 277 MET cc_start: 0.7972 (mmm) cc_final: 0.7676 (mmm) REVERT: G 283 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6734 (mm-30) REVERT: G 288 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7192 (tpt170) REVERT: G 290 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7545 (mtp85) REVERT: G 293 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6950 (tm-30) REVERT: G 294 ARG cc_start: 0.5902 (tmt-80) cc_final: 0.4774 (tmt170) REVERT: G 312 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 314 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8252 (pp) REVERT: G 318 LEU cc_start: 0.8877 (tp) cc_final: 0.8520 (tp) REVERT: G 327 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8042 (tm-30) REVERT: G 333 MET cc_start: 0.8487 (ptm) cc_final: 0.7651 (ptp) REVERT: G 342 GLU cc_start: 0.7905 (mp0) cc_final: 0.7366 (mp0) REVERT: G 344 GLU cc_start: 0.8156 (tp30) cc_final: 0.6630 (tp30) REVERT: G 347 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8189 (tm-30) REVERT: G 349 PHE cc_start: 0.8952 (t80) cc_final: 0.8647 (t80) REVERT: G 355 MET cc_start: 0.7990 (tpp) cc_final: 0.7049 (tpp) REVERT: G 359 LEU cc_start: 0.8969 (mt) cc_final: 0.8486 (mm) REVERT: G 417 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8395 (mtm-85) REVERT: G 418 ASP cc_start: 0.8317 (t70) cc_final: 0.7925 (t70) REVERT: G 419 CYS cc_start: 0.8716 (m) cc_final: 0.8117 (m) REVERT: G 422 LEU cc_start: 0.8822 (mt) cc_final: 0.8339 (mp) REVERT: G 423 PHE cc_start: 0.8654 (t80) cc_final: 0.8180 (t80) REVERT: G 425 CYS cc_start: 0.8876 (m) cc_final: 0.8541 (m) REVERT: G 426 TYR cc_start: 0.8639 (t80) cc_final: 0.8412 (t80) REVERT: G 429 GLN cc_start: 0.8409 (tt0) cc_final: 0.8027 (tt0) REVERT: G 432 MET cc_start: 0.7846 (mmm) cc_final: 0.7514 (mmm) REVERT: G 437 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8120 (tm-30) REVERT: G 442 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7359 (mtp-110) REVERT: G 443 ASN cc_start: 0.8223 (m-40) cc_final: 0.7920 (m-40) REVERT: G 445 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8378 (mptp) REVERT: G 448 GLN cc_start: 0.8386 (mt0) cc_final: 0.7543 (mt0) REVERT: G 449 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7645 (mmmm) REVERT: G 452 LYS cc_start: 0.8638 (mttm) cc_final: 0.8068 (mttm) REVERT: G 453 GLN cc_start: 0.8376 (mt0) cc_final: 0.7999 (mp10) REVERT: G 456 LYS cc_start: 0.9254 (tmtm) cc_final: 0.8830 (tmtm) REVERT: G 459 TRP cc_start: 0.8407 (m100) cc_final: 0.8136 (m100) REVERT: G 478 GLU cc_start: 0.8542 (pm20) cc_final: 0.8207 (pm20) REVERT: G 482 LYS cc_start: 0.8502 (tptp) cc_final: 0.7336 (tptp) REVERT: G 483 THR cc_start: 0.8854 (t) cc_final: 0.8585 (p) REVERT: G 486 GLN cc_start: 0.7849 (mm110) cc_final: 0.6797 (mm110) REVERT: G 490 ASP cc_start: 0.7807 (p0) cc_final: 0.7573 (p0) REVERT: G 495 SER cc_start: 0.8714 (m) cc_final: 0.8231 (p) REVERT: G 497 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8540 (mm) REVERT: G 498 GLN cc_start: 0.8659 (tp40) cc_final: 0.7639 (tp40) REVERT: G 501 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8060 (ptp-110) REVERT: G 502 ASN cc_start: 0.8170 (t0) cc_final: 0.7306 (t0) REVERT: G 504 ILE cc_start: 0.8683 (mm) cc_final: 0.8329 (mm) REVERT: G 506 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7568 (mm-30) REVERT: G 507 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8093 (mmm160) REVERT: G 540 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8541 (mm) REVERT: F 167 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5932 (pt) REVERT: F 173 PHE cc_start: 0.7921 (m-80) cc_final: 0.7624 (m-80) REVERT: F 175 GLN cc_start: 0.7393 (tm130) cc_final: 0.6812 (tm-30) REVERT: F 176 ASN cc_start: 0.8230 (m-40) cc_final: 0.7956 (m110) REVERT: F 191 ASP cc_start: 0.8427 (p0) cc_final: 0.7732 (p0) REVERT: F 192 LYS cc_start: 0.8673 (mmtt) cc_final: 0.7888 (mmtt) REVERT: F 193 GLN cc_start: 0.8684 (mm110) cc_final: 0.8418 (mm110) REVERT: F 194 LEU cc_start: 0.8771 (mt) cc_final: 0.8446 (mm) REVERT: F 197 ARG cc_start: 0.7675 (ptp-170) cc_final: 0.7356 (ptp-110) REVERT: F 198 GLN cc_start: 0.8273 (pm20) cc_final: 0.7809 (tp40) REVERT: F 215 PHE cc_start: 0.6722 (m-80) cc_final: 0.6428 (m-80) REVERT: F 253 LEU cc_start: 0.9054 (mm) cc_final: 0.8784 (mt) REVERT: F 271 ASN cc_start: 0.8475 (p0) cc_final: 0.8026 (p0) REVERT: F 277 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: F 284 LEU cc_start: 0.6880 (mt) cc_final: 0.6190 (tt) REVERT: F 325 ASP cc_start: 0.8006 (m-30) cc_final: 0.7682 (m-30) REVERT: F 327 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8094 (mm-30) REVERT: F 333 MET cc_start: 0.7809 (tpp) cc_final: 0.7557 (mpp) REVERT: F 334 MET cc_start: 0.8188 (tpt) cc_final: 0.7843 (tpt) REVERT: F 342 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7794 (mm-30) REVERT: F 346 MET cc_start: 0.7725 (mtt) cc_final: 0.7073 (mtt) REVERT: F 349 PHE cc_start: 0.8701 (t80) cc_final: 0.7837 (t80) REVERT: F 355 MET cc_start: 0.8047 (tpp) cc_final: 0.6735 (tpp) REVERT: F 356 GLN cc_start: 0.8591 (tt0) cc_final: 0.8127 (tm-30) REVERT: F 357 ARG cc_start: 0.8510 (ttt180) cc_final: 0.8047 (ttt-90) REVERT: F 358 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8091 (mtpp) REVERT: F 359 LEU cc_start: 0.9082 (mm) cc_final: 0.8431 (mm) REVERT: F 360 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 365 TYR cc_start: 0.8147 (m-80) cc_final: 0.7882 (m-80) REVERT: F 369 GLN cc_start: 0.6787 (tm-30) cc_final: 0.5934 (tm-30) REVERT: F 373 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7684 (ttp80) REVERT: F 383 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8313 (mt) REVERT: F 394 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: F 405 SER cc_start: 0.8721 (t) cc_final: 0.8514 (p) REVERT: F 407 LEU cc_start: 0.8859 (mt) cc_final: 0.8652 (mt) REVERT: F 419 CYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8367 (p) REVERT: F 427 THR cc_start: 0.8870 (p) cc_final: 0.8579 (t) REVERT: F 434 VAL cc_start: 0.8334 (p) cc_final: 0.8095 (m) REVERT: F 437 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: F 446 GLU cc_start: 0.8396 (tt0) cc_final: 0.7868 (pt0) REVERT: F 448 GLN cc_start: 0.8784 (mt0) cc_final: 0.8256 (mt0) REVERT: F 485 GLN cc_start: 0.7783 (mt0) cc_final: 0.7194 (mt0) REVERT: F 494 GLN cc_start: 0.8296 (mm110) cc_final: 0.7496 (mt0) REVERT: F 495 SER cc_start: 0.8256 (t) cc_final: 0.7719 (p) REVERT: F 498 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7920 (tp-100) REVERT: F 499 ASN cc_start: 0.8326 (m-40) cc_final: 0.8069 (m-40) REVERT: F 501 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8263 (ttm110) REVERT: F 502 ASN cc_start: 0.7866 (t0) cc_final: 0.7388 (t0) REVERT: F 526 LYS cc_start: 0.5062 (ptpt) cc_final: 0.4758 (ptmt) REVERT: F 528 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6007 (mtm110) REVERT: F 539 TYR cc_start: 0.8203 (t80) cc_final: 0.7536 (t80) REVERT: F 576 ARG cc_start: 0.7488 (mmp80) cc_final: 0.7059 (mtm-85) REVERT: F 581 ASN cc_start: 0.8241 (t0) cc_final: 0.7809 (t0) REVERT: F 583 GLN cc_start: 0.8773 (mm110) cc_final: 0.8554 (mm110) REVERT: F 587 GLU cc_start: 0.8407 (tt0) cc_final: 0.8128 (tt0) REVERT: F 611 LYS cc_start: 0.8539 (pttt) cc_final: 0.8113 (mmtm) REVERT: F 616 LEU cc_start: 0.8194 (tt) cc_final: 0.7979 (mm) REVERT: F 617 TRP cc_start: 0.8213 (t60) cc_final: 0.7832 (t60) REVERT: F 621 TYR cc_start: 0.8600 (t80) cc_final: 0.8253 (t80) REVERT: F 622 LEU cc_start: 0.8838 (mm) cc_final: 0.8478 (mt) REVERT: F 623 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7508 (ttp80) REVERT: F 628 GLU cc_start: 0.8288 (pt0) cc_final: 0.7581 (pt0) REVERT: F 646 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7964 (t0) REVERT: F 672 GLU cc_start: 0.8207 (pp20) cc_final: 0.7792 (pp20) REVERT: F 676 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7833 (ttm-80) outliers start: 38 outliers final: 20 residues processed: 398 average time/residue: 0.1053 time to fit residues: 53.1528 Evaluate side-chains 415 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 380 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 314 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU 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 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 181 LEU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 383 LEU 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 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 507 ARG 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 650 THR Chi-restraints excluded: chain F residue 658 HIS 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 50 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- 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 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099489 restraints weight = 15102.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103272 restraints weight = 7781.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105854 restraints weight = 4801.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107612 restraints weight = 3329.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108812 restraints weight = 2520.292| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6998 Z= 0.134 Angle : 0.816 12.361 9480 Z= 0.392 Chirality : 0.045 0.201 1059 Planarity : 0.006 0.094 1227 Dihedral : 4.852 55.631 936 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.81 % Allowed : 33.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.30), residues: 835 helix: 1.39 (0.24), residues: 471 sheet: -0.58 (1.88), residues: 12 loop : -1.26 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 330 TYR 0.028 0.001 TYR F 546 PHE 0.019 0.001 PHE G 503 TRP 0.018 0.002 TRP F 435 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6996) covalent geometry : angle 0.81609 ( 9476) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.89206 ( 4) hydrogen bonds : bond 0.03851 ( 342) hydrogen bonds : angle 4.43590 ( 984) ********************** 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 408 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 372 time to evaluate : 0.273 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: 0.7139 (m-10) cc_final: 0.6924 (m-10) REVERT: G 182 SER cc_start: 0.8258 (p) cc_final: 0.7532 (t) REVERT: G 192 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8567 (mtmt) REVERT: G 193 GLN cc_start: 0.8678 (mp10) cc_final: 0.8263 (mp10) REVERT: G 201 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7995 (m) REVERT: G 204 ASP cc_start: 0.7672 (t70) cc_final: 0.7281 (t0) REVERT: G 223 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7921 (mtmm) REVERT: G 258 ARG cc_start: 0.6850 (mtt180) cc_final: 0.6492 (mtt180) REVERT: G 272 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8536 (mm) REVERT: G 277 MET cc_start: 0.7929 (mmm) cc_final: 0.7672 (mmm) REVERT: G 283 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6709 (mm-30) REVERT: G 288 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7171 (tpt170) REVERT: G 290 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7539 (mtp85) REVERT: G 293 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6936 (tm-30) REVERT: G 294 ARG cc_start: 0.5878 (tmt-80) cc_final: 0.4664 (tmt170) REVERT: G 312 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 314 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8239 (pp) REVERT: G 320 THR cc_start: 0.8474 (t) cc_final: 0.7970 (m) REVERT: G 327 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8044 (tm-30) REVERT: G 333 MET cc_start: 0.8470 (ptm) cc_final: 0.7605 (ptp) REVERT: G 342 GLU cc_start: 0.7902 (mp0) cc_final: 0.7347 (mp0) REVERT: G 344 GLU cc_start: 0.8136 (tp30) cc_final: 0.6580 (tp30) REVERT: G 347 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8141 (tm-30) REVERT: G 349 PHE cc_start: 0.8935 (t80) cc_final: 0.8457 (t80) REVERT: G 355 MET cc_start: 0.7989 (tpp) cc_final: 0.7028 (tpp) REVERT: G 359 LEU cc_start: 0.8950 (mt) cc_final: 0.8489 (mm) REVERT: G 412 ARG cc_start: 0.8593 (ttt180) cc_final: 0.7953 (ttt-90) REVERT: G 417 ARG cc_start: 0.8695 (mtm110) cc_final: 0.8343 (mtm-85) REVERT: G 419 CYS cc_start: 0.8749 (m) cc_final: 0.8212 (m) REVERT: G 422 LEU cc_start: 0.8762 (mt) cc_final: 0.8197 (mp) REVERT: G 423 PHE cc_start: 0.8640 (t80) cc_final: 0.8185 (t80) REVERT: G 425 CYS cc_start: 0.8820 (m) cc_final: 0.8534 (m) REVERT: G 426 TYR cc_start: 0.8631 (t80) cc_final: 0.8403 (t80) REVERT: G 429 GLN cc_start: 0.8411 (tt0) cc_final: 0.8040 (tt0) REVERT: G 432 MET cc_start: 0.7810 (mmm) cc_final: 0.7475 (mmm) REVERT: G 437 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8077 (tm-30) REVERT: G 443 ASN cc_start: 0.8173 (m-40) cc_final: 0.7818 (m-40) REVERT: G 445 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8403 (mptp) REVERT: G 448 GLN cc_start: 0.8367 (mt0) cc_final: 0.7505 (mt0) REVERT: G 449 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7636 (mmmm) REVERT: G 452 LYS cc_start: 0.8600 (mttm) cc_final: 0.8037 (mttm) REVERT: G 453 GLN cc_start: 0.8326 (mt0) cc_final: 0.7829 (mp10) REVERT: G 456 LYS cc_start: 0.9243 (tmtm) cc_final: 0.8792 (tmtm) REVERT: G 478 GLU cc_start: 0.8538 (pm20) cc_final: 0.8217 (pm20) REVERT: G 482 LYS cc_start: 0.8503 (tptp) cc_final: 0.7463 (tptp) REVERT: G 486 GLN cc_start: 0.7831 (mm110) cc_final: 0.6834 (mm110) REVERT: G 490 ASP cc_start: 0.7823 (p0) cc_final: 0.7581 (p0) REVERT: G 495 SER cc_start: 0.8714 (m) cc_final: 0.8229 (p) REVERT: G 497 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8529 (mm) REVERT: G 498 GLN cc_start: 0.8647 (tp40) cc_final: 0.7672 (tp40) REVERT: G 501 ARG cc_start: 0.8639 (ttp-170) cc_final: 0.8076 (ptp-110) REVERT: G 502 ASN cc_start: 0.8171 (t0) cc_final: 0.7242 (t0) REVERT: G 504 ILE cc_start: 0.8684 (mm) cc_final: 0.8323 (mm) REVERT: G 506 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7546 (mm-30) REVERT: G 507 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8046 (mmm160) REVERT: G 526 LYS cc_start: 0.7689 (pttt) cc_final: 0.6751 (tmmt) REVERT: G 540 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8208 (pp) REVERT: F 167 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5735 (pt) REVERT: F 173 PHE cc_start: 0.7900 (m-80) cc_final: 0.7595 (m-80) REVERT: F 175 GLN cc_start: 0.7390 (tm130) cc_final: 0.7062 (tm-30) REVERT: F 176 ASN cc_start: 0.8229 (m-40) cc_final: 0.7931 (m110) REVERT: F 177 CYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7832 (m) REVERT: F 191 ASP cc_start: 0.8413 (p0) cc_final: 0.7717 (p0) REVERT: F 192 LYS cc_start: 0.8675 (mmtt) cc_final: 0.7880 (mmtt) REVERT: F 193 GLN cc_start: 0.8665 (mm110) cc_final: 0.8397 (mm110) REVERT: F 194 LEU cc_start: 0.8673 (mt) cc_final: 0.8411 (mm) REVERT: F 197 ARG cc_start: 0.7661 (ptp-170) cc_final: 0.7327 (ptp-110) REVERT: F 198 GLN cc_start: 0.8248 (pm20) cc_final: 0.7796 (tp40) REVERT: F 215 PHE cc_start: 0.6706 (m-80) cc_final: 0.6424 (m-80) REVERT: F 253 LEU cc_start: 0.9064 (mm) cc_final: 0.8807 (mt) REVERT: F 271 ASN cc_start: 0.8443 (p0) cc_final: 0.8136 (p0) REVERT: F 284 LEU cc_start: 0.6758 (mt) cc_final: 0.6105 (tt) REVERT: F 325 ASP cc_start: 0.8071 (m-30) cc_final: 0.7808 (m-30) REVERT: F 333 MET cc_start: 0.7867 (tpp) cc_final: 0.7576 (mpp) REVERT: F 334 MET cc_start: 0.8186 (tpt) cc_final: 0.7827 (tpt) REVERT: F 342 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7824 (mm-30) REVERT: F 346 MET cc_start: 0.7628 (mtt) cc_final: 0.7015 (mtt) REVERT: F 349 PHE cc_start: 0.8720 (t80) cc_final: 0.7859 (t80) REVERT: F 355 MET cc_start: 0.8050 (tpp) cc_final: 0.7086 (tpp) REVERT: F 356 GLN cc_start: 0.8598 (tt0) cc_final: 0.8136 (tm-30) REVERT: F 357 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8007 (ttt-90) REVERT: F 358 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8123 (mtpp) REVERT: F 360 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8290 (mt-10) REVERT: F 369 GLN cc_start: 0.6761 (tm-30) cc_final: 0.5774 (tm-30) REVERT: F 373 ARG cc_start: 0.8171 (ttt180) cc_final: 0.7711 (ttp80) REVERT: F 394 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7078 (t-90) REVERT: F 405 SER cc_start: 0.8677 (t) cc_final: 0.8460 (p) REVERT: F 407 LEU cc_start: 0.8861 (mt) cc_final: 0.8660 (mt) REVERT: F 419 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8333 (p) REVERT: F 422 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8379 (mp) REVERT: F 427 THR cc_start: 0.8865 (p) cc_final: 0.8583 (t) REVERT: F 434 VAL cc_start: 0.8315 (p) cc_final: 0.8068 (m) REVERT: F 437 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7712 (mm110) REVERT: F 446 GLU cc_start: 0.8339 (tt0) cc_final: 0.7851 (pt0) REVERT: F 448 GLN cc_start: 0.8753 (mt0) cc_final: 0.8271 (mt0) REVERT: F 484 LEU cc_start: 0.8606 (mt) cc_final: 0.8375 (mt) REVERT: F 494 GLN cc_start: 0.8267 (mm110) cc_final: 0.7446 (mt0) REVERT: F 495 SER cc_start: 0.8239 (t) cc_final: 0.7677 (p) REVERT: F 498 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7853 (tp-100) REVERT: F 499 ASN cc_start: 0.8320 (m-40) cc_final: 0.8058 (m-40) REVERT: F 501 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8243 (ttm110) REVERT: F 502 ASN cc_start: 0.7862 (t0) cc_final: 0.7370 (t0) REVERT: F 503 PHE cc_start: 0.8523 (t80) cc_final: 0.8293 (t80) REVERT: F 526 LYS cc_start: 0.5232 (ptpt) cc_final: 0.4891 (ptmt) REVERT: F 528 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.5874 (mtm110) REVERT: F 539 TYR cc_start: 0.8168 (t80) cc_final: 0.7532 (t80) REVERT: F 576 ARG cc_start: 0.7474 (mmp80) cc_final: 0.7190 (mtm-85) REVERT: F 581 ASN cc_start: 0.8252 (t0) cc_final: 0.7817 (t0) REVERT: F 583 GLN cc_start: 0.8761 (mm110) cc_final: 0.8551 (mm110) REVERT: F 587 GLU cc_start: 0.8345 (tt0) cc_final: 0.8068 (tt0) REVERT: F 611 LYS cc_start: 0.8542 (pttt) cc_final: 0.8128 (mmtp) REVERT: F 616 LEU cc_start: 0.8175 (tt) cc_final: 0.7968 (mm) REVERT: F 617 TRP cc_start: 0.8197 (t60) cc_final: 0.7834 (t60) REVERT: F 622 LEU cc_start: 0.8838 (mm) cc_final: 0.8568 (mt) REVERT: F 623 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7535 (ttp80) REVERT: F 628 GLU cc_start: 0.8298 (pt0) cc_final: 0.7582 (pt0) REVERT: F 646 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7964 (t0) REVERT: F 672 GLU cc_start: 0.8195 (pp20) cc_final: 0.7770 (pp20) REVERT: F 676 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7815 (ttm-80) outliers start: 36 outliers final: 16 residues processed: 382 average time/residue: 0.1022 time to fit residues: 49.4491 Evaluate side-chains 399 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 497 LEU 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 214 ILE 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 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 507 ARG 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 690 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 HIS F 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099369 restraints weight = 15191.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103130 restraints weight = 7782.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105662 restraints weight = 4775.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107413 restraints weight = 3289.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108639 restraints weight = 2471.960| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6998 Z= 0.139 Angle : 0.846 17.305 9480 Z= 0.401 Chirality : 0.046 0.182 1059 Planarity : 0.006 0.089 1227 Dihedral : 4.869 52.611 936 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.54 % Allowed : 34.98 % Favored : 60.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.30), residues: 835 helix: 1.32 (0.24), residues: 474 sheet: -0.67 (1.85), residues: 12 loop : -1.29 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 636 TYR 0.030 0.001 TYR F 546 PHE 0.025 0.001 PHE G 462 TRP 0.028 0.003 TRP G 459 HIS 0.005 0.001 HIS F 633 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6996) covalent geometry : angle 0.84630 ( 9476) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.72026 ( 4) hydrogen bonds : bond 0.03825 ( 342) hydrogen bonds : angle 4.47505 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1631.83 seconds wall clock time: 28 minutes 42.78 seconds (1722.78 seconds total)