Starting phenix.real_space_refine on Tue Mar 11 17:20:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzd_39690/03_2025/8yzd_39690.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.325 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 37 5.16 5 C 4128 2.51 5 N 1069 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6436 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 4.71, per 1000 atoms: 0.73 Number of scatterers: 6436 At special positions: 0 Unit cell: (84.49, 101.15, 116.62, 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 37 16.00 O 1202 8.00 N 1069 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 54.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.946A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.971A pdb=" N GLN B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 77 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.853A pdb=" N MET B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.520A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 88 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.997A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.571A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.605A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.877A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.712A pdb=" N LYS B 247 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.518A pdb=" N LEU B 278 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.843A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.547A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.713A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.505A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.634A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.166A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.854A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.626A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 600 Proline residue: B 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.021A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.849A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.718A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 294 hydrogen bonds defined for protein. 846 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: 2.31 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2060 1.34 - 1.46: 1621 1.46 - 1.58: 2886 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6625 Sorted by residual: bond pdb=" C GLU B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.06e+00 bond pdb=" CA LYS A 378 " pdb=" C LYS A 378 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.08e-02 8.57e+03 2.91e+00 bond pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.26e-02 6.30e+03 1.67e+00 bond pdb=" C ALA A 372 " pdb=" O ALA A 372 " ideal model delta sigma weight residual 1.238 1.225 0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 1.519 1.509 0.010 1.32e-02 5.74e+03 5.63e-01 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 8920 1.66 - 3.33: 70 3.33 - 4.99: 10 4.99 - 6.65: 3 6.65 - 8.31: 1 Bond angle restraints: 9004 Sorted by residual: angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 111.14 102.83 8.31 1.08e+00 8.57e-01 5.93e+01 angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 113.88 107.25 6.63 1.23e+00 6.61e-01 2.91e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 109.46 115.41 -5.95 1.66e+00 3.63e-01 1.28e+01 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 109.03 113.66 -4.63 1.62e+00 3.81e-01 8.16e+00 angle pdb=" C LYS A 378 " pdb=" CA LYS A 378 " pdb=" CB LYS A 378 " ideal model delta sigma weight residual 111.70 108.19 3.51 1.31e+00 5.83e-01 7.19e+00 ... (remaining 8999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3790 17.45 - 34.90: 102 34.90 - 52.36: 11 52.36 - 69.81: 1 69.81 - 87.26: 2 Dihedral angle restraints: 3906 sinusoidal: 1579 harmonic: 2327 Sorted by residual: dihedral pdb=" CB GLU B 495 " pdb=" CG GLU B 495 " pdb=" CD GLU B 495 " pdb=" OE1 GLU B 495 " ideal model delta sinusoidal sigma weight residual 0.00 87.26 -87.26 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " ideal model delta sinusoidal sigma weight residual 60.00 114.24 -54.24 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N GLN B 60 " pdb=" CA GLN B 60 " pdb=" CB GLN B 60 " pdb=" CG GLN B 60 " ideal model delta sinusoidal sigma weight residual -60.00 -112.24 52.24 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 828 0.056 - 0.112: 98 0.112 - 0.168: 7 0.168 - 0.225: 0 0.225 - 0.281: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 931 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 369 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C TYR A 369 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 369 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 582 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 583 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 499 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 500 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " -0.016 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1894 2.82 - 3.34: 5529 3.34 - 3.86: 9786 3.86 - 4.38: 11195 4.38 - 4.90: 20139 Nonbonded interactions: 48543 Sorted by model distance: nonbonded pdb=" OG1 THR B 20 " pdb=" OE1 GLU B 23 " model vdw 2.299 3.040 nonbonded pdb=" O ASN B 117 " pdb=" ND2 ASN B 121 " model vdw 2.360 3.120 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR B 41 " model vdw 2.362 3.040 nonbonded pdb=" O SER B 47 " pdb=" ND2 ASN B 51 " model vdw 2.365 3.120 nonbonded pdb=" O VAL B 59 " pdb=" ND2 ASN B 63 " model vdw 2.391 3.120 ... (remaining 48538 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.002 0.041 6625 Z= 0.093 Angle : 0.416 8.314 9004 Z= 0.245 Chirality : 0.038 0.281 934 Planarity : 0.003 0.036 1167 Dihedral : 7.782 87.258 2394 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 3.02 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.27), residues: 788 helix: -0.02 (0.26), residues: 397 sheet: 1.26 (0.68), residues: 45 loop : -2.88 (0.25), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 165 HIS 0.001 0.000 HIS B 374 PHE 0.008 0.001 PHE A 375 TYR 0.007 0.001 TYR B 516 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8202 (m-30) cc_final: 0.7990 (m-30) REVERT: B 323 MET cc_start: 0.8501 (mmt) cc_final: 0.7735 (mmt) outliers start: 9 outliers final: 3 residues processed: 151 average time/residue: 0.2522 time to fit residues: 47.0762 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 199 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 493 GLN A 506 GLN B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.044511 restraints weight = 19785.348| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 1.84 r_work: 0.2482 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6625 Z= 0.218 Angle : 0.547 6.604 9004 Z= 0.288 Chirality : 0.042 0.138 934 Planarity : 0.004 0.033 1167 Dihedral : 4.450 43.466 867 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 6.47 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 788 helix: 1.12 (0.27), residues: 391 sheet: 1.76 (0.75), residues: 40 loop : -2.34 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS B 34 PHE 0.016 0.002 PHE B 438 TYR 0.022 0.002 TYR B 385 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: B 190 MET cc_start: 0.9203 (ttp) cc_final: 0.8950 (tmm) REVERT: B 323 MET cc_start: 0.8898 (mmt) cc_final: 0.8295 (mmt) REVERT: B 512 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8633 (m-80) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.1845 time to fit residues: 23.4953 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 HIS ** 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 = 0.2663 r_free = 0.2663 target = 0.048099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.041357 restraints weight = 20164.233| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 1.84 r_work: 0.2390 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2303 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6625 Z= 0.251 Angle : 0.568 6.499 9004 Z= 0.300 Chirality : 0.042 0.135 934 Planarity : 0.004 0.035 1167 Dihedral : 4.864 43.086 867 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 7.33 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.29), residues: 788 helix: 1.43 (0.27), residues: 384 sheet: 1.82 (0.81), residues: 40 loop : -2.04 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.005 0.001 HIS B 493 PHE 0.016 0.002 PHE B 438 TYR 0.022 0.002 TYR B 385 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.794 Fit side-chains REVERT: A 364 ASP cc_start: 0.8768 (t0) cc_final: 0.8447 (p0) REVERT: B 131 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8413 (ttpp) REVERT: B 190 MET cc_start: 0.9231 (ttp) cc_final: 0.8961 (tmm) REVERT: B 199 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8693 (t80) REVERT: B 323 MET cc_start: 0.8923 (mmt) cc_final: 0.8311 (mmt) REVERT: B 512 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8648 (m-80) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 0.1913 time to fit residues: 21.5703 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.047701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.040982 restraints weight = 20185.995| |-----------------------------------------------------------------------------| r_work (start): 0.2460 rms_B_bonded: 1.83 r_work: 0.2379 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2292 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6625 Z= 0.235 Angle : 0.546 6.628 9004 Z= 0.288 Chirality : 0.042 0.126 934 Planarity : 0.004 0.030 1167 Dihedral : 4.936 46.059 867 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.02 % Allowed : 8.48 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 788 helix: 1.45 (0.27), residues: 391 sheet: 1.62 (0.79), residues: 45 loop : -1.91 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.002 PHE A 375 TYR 0.019 0.001 TYR B 385 ARG 0.004 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8775 (t0) cc_final: 0.8419 (p0) REVERT: B 190 MET cc_start: 0.9261 (ttp) cc_final: 0.8992 (tmm) REVERT: B 199 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8611 (t80) REVERT: B 497 TYR cc_start: 0.7699 (m-10) cc_final: 0.7470 (m-80) REVERT: B 512 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8623 (m-80) outliers start: 21 outliers final: 13 residues processed: 87 average time/residue: 0.1923 time to fit residues: 22.4893 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.048357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.041627 restraints weight = 20059.432| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 1.84 r_work: 0.2398 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6625 Z= 0.196 Angle : 0.518 6.126 9004 Z= 0.273 Chirality : 0.040 0.130 934 Planarity : 0.004 0.028 1167 Dihedral : 4.933 50.475 867 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 9.63 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 788 helix: 1.57 (0.27), residues: 398 sheet: 1.68 (0.79), residues: 45 loop : -1.71 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 PHE 0.010 0.001 PHE A 375 TYR 0.015 0.001 TYR B 516 ARG 0.004 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8743 (t0) cc_final: 0.8414 (p0) REVERT: B 199 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8620 (t80) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.1865 time to fit residues: 21.2254 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.045786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.039198 restraints weight = 20128.359| |-----------------------------------------------------------------------------| r_work (start): 0.2408 rms_B_bonded: 1.83 r_work: 0.2325 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2239 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6625 Z= 0.280 Angle : 0.585 7.285 9004 Z= 0.311 Chirality : 0.042 0.126 934 Planarity : 0.004 0.030 1167 Dihedral : 5.199 52.826 867 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.73 % Allowed : 10.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 788 helix: 1.49 (0.27), residues: 391 sheet: 1.41 (0.76), residues: 45 loop : -1.70 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.005 0.001 HIS B 374 PHE 0.022 0.002 PHE A 375 TYR 0.021 0.002 TYR B 385 ARG 0.003 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8773 (t0) cc_final: 0.8523 (p0) REVERT: B 190 MET cc_start: 0.9261 (ttp) cc_final: 0.8957 (tmm) REVERT: B 512 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8704 (m-80) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 0.2039 time to fit residues: 23.8145 Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.045338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.038792 restraints weight = 20154.285| |-----------------------------------------------------------------------------| r_work (start): 0.2397 rms_B_bonded: 1.82 r_work: 0.2314 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2228 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6625 Z= 0.298 Angle : 0.599 7.460 9004 Z= 0.320 Chirality : 0.043 0.135 934 Planarity : 0.004 0.032 1167 Dihedral : 5.013 55.743 865 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.30 % Allowed : 11.06 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.29), residues: 788 helix: 1.43 (0.27), residues: 393 sheet: 1.49 (0.75), residues: 45 loop : -1.76 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.005 0.001 HIS B 239 PHE 0.024 0.002 PHE A 375 TYR 0.031 0.002 TYR B 158 ARG 0.004 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8713 (t0) cc_final: 0.8497 (p0) REVERT: B 190 MET cc_start: 0.9251 (ttp) cc_final: 0.8955 (tmm) REVERT: B 512 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8684 (m-80) outliers start: 23 outliers final: 17 residues processed: 85 average time/residue: 0.2008 time to fit residues: 22.9373 Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 601 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.046707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.040122 restraints weight = 20113.331| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 1.82 r_work: 0.2354 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2271 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6625 Z= 0.216 Angle : 0.552 6.691 9004 Z= 0.293 Chirality : 0.041 0.132 934 Planarity : 0.004 0.031 1167 Dihedral : 4.849 56.478 865 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 12.50 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.30), residues: 788 helix: 1.62 (0.27), residues: 392 sheet: 1.62 (0.78), residues: 45 loop : -1.65 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.022 0.001 PHE A 375 TYR 0.026 0.001 TYR B 158 ARG 0.002 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8750 (t0) cc_final: 0.8538 (p0) outliers start: 20 outliers final: 12 residues processed: 83 average time/residue: 0.1845 time to fit residues: 20.8514 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.046936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.040347 restraints weight = 20293.748| |-----------------------------------------------------------------------------| r_work (start): 0.2442 rms_B_bonded: 1.83 r_work: 0.2360 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6625 Z= 0.220 Angle : 0.554 6.771 9004 Z= 0.295 Chirality : 0.041 0.134 934 Planarity : 0.004 0.031 1167 Dihedral : 4.807 59.417 865 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.01 % Allowed : 13.65 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 788 helix: 1.69 (0.27), residues: 394 sheet: 1.64 (0.79), residues: 45 loop : -1.54 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE A 375 TYR 0.025 0.001 TYR B 158 ARG 0.002 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8744 (t0) cc_final: 0.8529 (p0) REVERT: B 512 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8664 (m-80) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.1955 time to fit residues: 21.0501 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.0040 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.047453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.040852 restraints weight = 20488.797| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 1.83 r_work: 0.2376 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6625 Z= 0.199 Angle : 0.532 6.827 9004 Z= 0.284 Chirality : 0.041 0.144 934 Planarity : 0.004 0.032 1167 Dihedral : 4.707 58.123 865 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.58 % Allowed : 14.51 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 788 helix: 1.79 (0.27), residues: 394 sheet: 1.66 (0.80), residues: 45 loop : -1.49 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 477 HIS 0.003 0.001 HIS B 374 PHE 0.015 0.001 PHE A 375 TYR 0.025 0.001 TYR B 158 ARG 0.004 0.000 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8746 (t0) cc_final: 0.8529 (p0) REVERT: A 375 PHE cc_start: 0.8572 (m-80) cc_final: 0.8302 (m-80) REVERT: B 512 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8570 (m-80) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.1878 time to fit residues: 21.0200 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.046303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.039751 restraints weight = 20744.336| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 1.86 r_work: 0.2341 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2253 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6625 Z= 0.236 Angle : 0.563 7.081 9004 Z= 0.302 Chirality : 0.042 0.142 934 Planarity : 0.004 0.031 1167 Dihedral : 4.815 57.304 865 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.72 % Allowed : 14.22 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 788 helix: 1.74 (0.27), residues: 392 sheet: 1.57 (0.79), residues: 45 loop : -1.52 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.015 0.001 PHE B 512 TYR 0.027 0.001 TYR B 158 ARG 0.003 0.000 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.40 seconds wall clock time: 61 minutes 57.98 seconds (3717.98 seconds total)