Starting phenix.real_space_refine on Wed Sep 17 06:55:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzd_39690/09_2025/8yzd_39690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzd_39690/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yzd_39690/09_2025/8yzd_39690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzd_39690/09_2025/8yzd_39690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yzd_39690/09_2025/8yzd_39690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzd_39690/09_2025/8yzd_39690.map" } resolution = 3.07 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= -0.008 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): 0.01s 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: 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: 1.32, per 1000 atoms: 0.21 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: 0.41 Conformation dependent library (CDL) restraints added in 331.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 0.81 Time building geometry restraints manager: 0.56 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: 2.190 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: 0.010 Set scattering table: 0.020 Process input model: 6.550 Find NCS groups from input model: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.170 ------------------------------------------------------------------------------- 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 6631 Z= 0.092 Angle : 0.416 8.314 9016 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 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: -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 ARG 0.002 0.000 ARG A 457 TYR 0.007 0.001 TYR B 516 PHE 0.008 0.001 PHE A 375 TRP 0.007 0.001 TRP B 165 HIS 0.001 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 6625) covalent geometry : angle 0.41585 ( 9004) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.63162 ( 12) hydrogen bonds : bond 0.16469 ( 294) hydrogen bonds : angle 5.66134 ( 846) *********************** 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 : 0.248 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: 0.1036 time to fit residues: 19.4917 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 : 0.220 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2741 r_free = 0.2741 target = 0.050945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.044175 restraints weight = 20107.840| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 1.85 r_work: 0.2473 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6631 Z= 0.154 Angle : 0.553 6.633 9016 Z= 0.292 Chirality : 0.042 0.138 934 Planarity : 0.004 0.032 1167 Dihedral : 4.493 43.534 867 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.59 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 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 (0.29), residues: 788 helix: 1.12 (0.27), residues: 391 sheet: 1.79 (0.76), residues: 40 loop : -2.34 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 346 TYR 0.023 0.002 TYR B 385 PHE 0.017 0.002 PHE B 438 TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS B 493 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6625) covalent geometry : angle 0.55189 ( 9004) SS BOND : bond 0.00406 ( 6) SS BOND : angle 1.20668 ( 12) hydrogen bonds : bond 0.06660 ( 294) hydrogen bonds : angle 4.20975 ( 846) *********************** 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 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 190 MET cc_start: 0.9218 (ttp) cc_final: 0.8960 (tmm) REVERT: B 323 MET cc_start: 0.8902 (mmt) cc_final: 0.8299 (mmt) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.0724 time to fit residues: 8.9816 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 534 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.2593 r_free = 0.2593 target = 0.045485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.038859 restraints weight = 20229.101| |-----------------------------------------------------------------------------| r_work (start): 0.2397 rms_B_bonded: 1.83 r_work: 0.2315 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2229 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6631 Z= 0.245 Angle : 0.666 7.343 9016 Z= 0.355 Chirality : 0.045 0.130 934 Planarity : 0.005 0.040 1167 Dihedral : 5.277 45.433 867 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.30 % Allowed : 7.33 % Favored : 89.37 % 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 (0.28), residues: 788 helix: 1.09 (0.26), residues: 390 sheet: 1.66 (0.78), residues: 40 loop : -2.16 (0.26), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 346 TYR 0.029 0.002 TYR B 385 PHE 0.018 0.002 PHE B 438 TRP 0.019 0.002 TRP A 353 HIS 0.005 0.002 HIS B 493 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 6625) covalent geometry : angle 0.66365 ( 9004) SS BOND : bond 0.00580 ( 6) SS BOND : angle 1.62399 ( 12) hydrogen bonds : bond 0.09086 ( 294) hydrogen bonds : angle 4.48927 ( 846) *********************** 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 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8857 (mtp-110) REVERT: A 364 ASP cc_start: 0.8785 (t0) cc_final: 0.8464 (p0) REVERT: B 190 MET cc_start: 0.9257 (ttp) cc_final: 0.8956 (tmm) REVERT: B 199 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8605 (t80) REVERT: B 323 MET cc_start: 0.8931 (mmt) cc_final: 0.8386 (mmt) outliers start: 23 outliers final: 15 residues processed: 84 average time/residue: 0.0756 time to fit residues: 8.6976 Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.2661 r_free = 0.2661 target = 0.048020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.041306 restraints weight = 20241.581| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 1.84 r_work: 0.2388 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2301 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6631 Z= 0.139 Angle : 0.528 6.424 9016 Z= 0.278 Chirality : 0.041 0.129 934 Planarity : 0.004 0.030 1167 Dihedral : 4.982 50.029 867 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.16 % Allowed : 9.20 % Favored : 88.65 % 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: 0.04 (0.29), residues: 788 helix: 1.41 (0.27), residues: 391 sheet: 1.66 (0.77), residues: 45 loop : -1.90 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.016 0.001 TYR B 516 PHE 0.018 0.001 PHE A 375 TRP 0.016 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6625) covalent geometry : angle 0.52640 ( 9004) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.29291 ( 12) hydrogen bonds : bond 0.06471 ( 294) hydrogen bonds : angle 4.19049 ( 846) *********************** 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 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8781 (t0) cc_final: 0.8464 (p0) REVERT: B 199 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8579 (t80) REVERT: B 497 TYR cc_start: 0.7755 (m-80) cc_final: 0.7501 (m-80) REVERT: B 512 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8512 (m-80) outliers start: 15 outliers final: 8 residues processed: 86 average time/residue: 0.0826 time to fit residues: 9.4760 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 0.0020 chunk 56 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.2673 r_free = 0.2673 target = 0.048509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.041786 restraints weight = 20304.766| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 1.85 r_work: 0.2401 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6631 Z= 0.129 Angle : 0.513 6.253 9016 Z= 0.269 Chirality : 0.040 0.131 934 Planarity : 0.004 0.030 1167 Dihedral : 4.934 55.160 867 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.16 % Allowed : 10.49 % Favored : 87.36 % 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: 0.30 (0.30), residues: 788 helix: 1.53 (0.27), residues: 399 sheet: 1.72 (0.77), residues: 45 loop : -1.71 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.014 0.001 TYR B 516 PHE 0.010 0.001 PHE A 375 TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6625) covalent geometry : angle 0.51131 ( 9004) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.13807 ( 12) hydrogen bonds : bond 0.06089 ( 294) hydrogen bonds : angle 4.09689 ( 846) *********************** 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 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8759 (t0) cc_final: 0.8446 (p0) REVERT: B 199 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8728 (t80) REVERT: B 512 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8536 (m-80) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.0789 time to fit residues: 8.5879 Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 0.0030 chunk 37 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 overall best weight: 0.3282 ------------------------------------------------------------------------------- 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 = 0.2721 r_free = 0.2721 target = 0.050293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.043601 restraints weight = 20122.591| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 1.84 r_work: 0.2454 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6631 Z= 0.108 Angle : 0.483 6.172 9016 Z= 0.250 Chirality : 0.039 0.127 934 Planarity : 0.003 0.028 1167 Dihedral : 4.710 58.865 867 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.72 % Allowed : 10.78 % Favored : 87.50 % 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: 0.70 (0.30), residues: 788 helix: 1.94 (0.28), residues: 386 sheet: 1.90 (0.78), residues: 45 loop : -1.48 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.013 0.001 TYR B 516 PHE 0.025 0.001 PHE A 375 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6625) covalent geometry : angle 0.48180 ( 9004) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.98970 ( 12) hydrogen bonds : bond 0.04961 ( 294) hydrogen bonds : angle 3.94347 ( 846) *********************** 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 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8707 (t0) cc_final: 0.8470 (p0) REVERT: B 512 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8550 (m-80) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.0750 time to fit residues: 8.5034 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 = 0.2593 r_free = 0.2593 target = 0.045431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.038856 restraints weight = 20429.696| |-----------------------------------------------------------------------------| r_work (start): 0.2399 rms_B_bonded: 1.83 r_work: 0.2315 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2228 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6631 Z= 0.208 Angle : 0.610 6.989 9016 Z= 0.324 Chirality : 0.043 0.143 934 Planarity : 0.004 0.030 1167 Dihedral : 4.850 52.116 865 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.73 % Allowed : 11.78 % Favored : 85.49 % 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: 0.33 (0.29), residues: 788 helix: 1.58 (0.27), residues: 391 sheet: 1.67 (0.75), residues: 45 loop : -1.63 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 169 TYR 0.032 0.002 TYR B 158 PHE 0.014 0.002 PHE B 438 TRP 0.014 0.002 TRP A 353 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6625) covalent geometry : angle 0.60809 ( 9004) SS BOND : bond 0.00467 ( 6) SS BOND : angle 1.45531 ( 12) hydrogen bonds : bond 0.08159 ( 294) hydrogen bonds : angle 4.29672 ( 846) *********************** 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 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8787 (t0) cc_final: 0.8529 (p0) REVERT: A 440 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8967 (mtpp) REVERT: B 190 MET cc_start: 0.9285 (ttp) cc_final: 0.8993 (tmm) REVERT: B 255 TYR cc_start: 0.8849 (m-10) cc_final: 0.8603 (m-10) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.0726 time to fit residues: 8.2887 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS 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 332 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.2649 r_free = 0.2649 target = 0.047499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.040862 restraints weight = 20332.414| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.85 r_work: 0.2375 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6631 Z= 0.139 Angle : 0.532 6.386 9016 Z= 0.280 Chirality : 0.041 0.136 934 Planarity : 0.004 0.030 1167 Dihedral : 4.288 26.130 863 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.01 % Allowed : 13.07 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.30), residues: 788 helix: 1.73 (0.27), residues: 392 sheet: 1.77 (0.76), residues: 45 loop : -1.56 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.024 0.001 TYR B 158 PHE 0.018 0.001 PHE A 375 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6625) covalent geometry : angle 0.53050 ( 9004) SS BOND : bond 0.00331 ( 6) SS BOND : angle 1.20382 ( 12) hydrogen bonds : bond 0.06342 ( 294) hydrogen bonds : angle 4.11687 ( 846) *********************** 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 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8754 (t0) cc_final: 0.8524 (p0) REVERT: B 512 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8536 (m-80) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.0870 time to fit residues: 9.4274 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 : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain B residue 601 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.2648 r_free = 0.2648 target = 0.047476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.040863 restraints weight = 20446.666| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.85 r_work: 0.2375 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6631 Z= 0.141 Angle : 0.543 6.964 9016 Z= 0.286 Chirality : 0.041 0.141 934 Planarity : 0.003 0.030 1167 Dihedral : 4.261 26.492 863 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.58 % Allowed : 13.65 % Favored : 84.77 % 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: 0.57 (0.30), residues: 788 helix: 1.75 (0.27), residues: 393 sheet: 1.75 (0.77), residues: 45 loop : -1.50 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.025 0.001 TYR B 158 PHE 0.023 0.001 PHE A 375 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6625) covalent geometry : angle 0.54161 ( 9004) SS BOND : bond 0.00326 ( 6) SS BOND : angle 1.17493 ( 12) hydrogen bonds : bond 0.06382 ( 294) hydrogen bonds : angle 4.10237 ( 846) *********************** 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 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8758 (t0) cc_final: 0.8519 (p0) REVERT: B 512 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8561 (m-80) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.0763 time to fit residues: 8.1597 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 49 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.046753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.040190 restraints weight = 20113.952| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 1.81 r_work: 0.2354 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6631 Z= 0.154 Angle : 0.556 7.005 9016 Z= 0.295 Chirality : 0.041 0.142 934 Planarity : 0.004 0.032 1167 Dihedral : 4.359 27.925 863 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.72 % Allowed : 13.65 % 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 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: 0.55 (0.30), residues: 788 helix: 1.75 (0.27), residues: 391 sheet: 1.66 (0.76), residues: 45 loop : -1.50 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.025 0.001 TYR B 158 PHE 0.020 0.001 PHE A 375 TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6625) covalent geometry : angle 0.55445 ( 9004) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.21987 ( 12) hydrogen bonds : bond 0.06815 ( 294) hydrogen bonds : angle 4.15256 ( 846) ********************** 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: 12 poor density : 72 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8693 (t0) cc_final: 0.8463 (p0) REVERT: B 190 MET cc_start: 0.9261 (ttp) cc_final: 0.8989 (tmm) REVERT: B 512 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8486 (m-80) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.0841 time to fit residues: 8.8476 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain B residue 601 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.2671 r_free = 0.2671 target = 0.048325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.041747 restraints weight = 20046.988| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 1.83 r_work: 0.2402 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6631 Z= 0.127 Angle : 0.529 7.154 9016 Z= 0.280 Chirality : 0.040 0.143 934 Planarity : 0.003 0.031 1167 Dihedral : 4.159 25.598 863 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.44 % Allowed : 13.94 % 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 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: 0.74 (0.30), residues: 788 helix: 1.88 (0.27), residues: 392 sheet: 1.82 (0.78), residues: 45 loop : -1.39 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.025 0.001 TYR B 158 PHE 0.018 0.001 PHE A 375 TRP 0.013 0.001 TRP B 477 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6625) covalent geometry : angle 0.52833 ( 9004) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.08423 ( 12) hydrogen bonds : bond 0.05694 ( 294) hydrogen bonds : angle 4.04767 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.74 seconds wall clock time: 27 minutes 6.43 seconds (1626.43 seconds total)