Starting phenix.real_space_refine on Fri Aug 22 15:45:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqq_39502/08_2025/8yqq_39502_trim.cif" } resolution = 3.95 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= 0.002 sd= 0.031 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 47 5.16 5 C 3217 2.51 5 N 883 2.21 5 O 994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2218 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain: "B" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2833 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.39, per 1000 atoms: 0.27 Number of scatterers: 5141 At special positions: 0 Unit cell: (68.04, 80.19, 134.46, 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 47 16.00 O 994 8.00 N 883 7.00 C 3217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.02 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.02 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=1.99 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=1.99 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=1.98 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=1.99 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.01 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.00 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.01 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " 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 Links applied NAG-ASN " NAG A 703 " - " ASN A 355 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 210.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 13.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.681A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.023A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.720A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.180A pdb=" N VAL A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.708A pdb=" N VAL A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.097A pdb=" N PHE A 572 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.951A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.519A pdb=" N TYR B 485 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 371 removed outlier: 6.282A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.686A pdb=" N PHE A 391 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 463 removed outlier: 4.225A pdb=" N ASP A 578 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 576 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.396A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.502A pdb=" N THR A 509 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.504A pdb=" N ARG B 150 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 167 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.744A pdb=" N CYS B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 328 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 383 removed outlier: 4.250A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 460 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 447 " --> pdb=" O TRP B 454 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 270 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: 0.76 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 885 1.32 - 1.45: 1510 1.45 - 1.57: 2825 1.57 - 1.70: 0 1.70 - 1.83: 56 Bond restraints: 5276 Sorted by residual: bond pdb=" CA SER A 563 " pdb=" CB SER A 563 " ideal model delta sigma weight residual 1.533 1.450 0.083 1.69e-02 3.50e+03 2.40e+01 bond pdb=" C PRO A 496 " pdb=" O PRO A 496 " ideal model delta sigma weight residual 1.233 1.194 0.039 9.90e-03 1.02e+04 1.56e+01 bond pdb=" N ILE A 588 " pdb=" CA ILE A 588 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" CA SER A 488 " pdb=" CB SER A 488 " ideal model delta sigma weight residual 1.531 1.476 0.055 1.53e-02 4.27e+03 1.31e+01 bond pdb=" C PRO A 490 " pdb=" O PRO A 490 " ideal model delta sigma weight residual 1.240 1.200 0.040 1.12e-02 7.97e+03 1.30e+01 ... (remaining 5271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 6625 2.37 - 4.74: 479 4.74 - 7.11: 65 7.11 - 9.48: 11 9.48 - 11.85: 3 Bond angle restraints: 7183 Sorted by residual: angle pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" C ARG A 447 " ideal model delta sigma weight residual 113.50 103.12 10.38 1.23e+00 6.61e-01 7.12e+01 angle pdb=" N PRO A 475 " pdb=" CA PRO A 475 " pdb=" C PRO A 475 " ideal model delta sigma weight residual 113.75 104.29 9.46 1.49e+00 4.50e-01 4.03e+01 angle pdb=" C THR A 602 " pdb=" CA THR A 602 " pdb=" CB THR A 602 " ideal model delta sigma weight residual 111.74 103.25 8.49 1.37e+00 5.33e-01 3.84e+01 angle pdb=" N GLN A 559 " pdb=" CA GLN A 559 " pdb=" C GLN A 559 " ideal model delta sigma weight residual 113.41 106.01 7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" CA HIS A 562 " pdb=" CB HIS A 562 " pdb=" CG HIS A 562 " ideal model delta sigma weight residual 113.80 119.33 -5.53 1.00e+00 1.00e+00 3.06e+01 ... (remaining 7178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 2963 23.97 - 47.94: 241 47.94 - 71.91: 41 71.91 - 95.87: 6 95.87 - 119.84: 4 Dihedral angle restraints: 3255 sinusoidal: 1380 harmonic: 1875 Sorted by residual: dihedral pdb=" CD ARG A 517 " pdb=" NE ARG A 517 " pdb=" CZ ARG A 517 " pdb=" NH1 ARG A 517 " ideal model delta sinusoidal sigma weight residual 0.00 86.60 -86.60 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 516 " pdb=" CB CYS A 516 " ideal model delta sinusoidal sigma weight residual 93.00 156.79 -63.79 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CD ARG A 585 " pdb=" NE ARG A 585 " pdb=" CZ ARG A 585 " pdb=" NH1 ARG A 585 " ideal model delta sinusoidal sigma weight residual 0.00 60.32 -60.32 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 560 0.069 - 0.139: 171 0.139 - 0.208: 43 0.208 - 0.278: 7 0.278 - 0.347: 1 Chirality restraints: 782 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 355 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ARG A 447 " pdb=" N ARG A 447 " pdb=" C ARG A 447 " pdb=" CB ARG A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN A 598 " pdb=" N ASN A 598 " pdb=" C ASN A 598 " pdb=" CB ASN A 598 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 779 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 355 " 0.115 2.00e-02 2.50e+03 4.11e-01 2.11e+03 pdb=" CG ASN A 355 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 355 " 0.401 2.00e-02 2.50e+03 pdb=" ND2 ASN A 355 " -0.756 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B 502 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG A 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.156 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 1695 2.83 - 3.52: 6799 3.52 - 4.21: 12060 4.21 - 4.90: 19794 Nonbonded interactions: 40351 Sorted by model distance: nonbonded pdb=" O3 NAG B 501 " pdb=" O5 NAG B 502 " model vdw 1.447 3.040 nonbonded pdb=" O ASN A 605 " pdb=" N LEU A 607 " model vdw 1.913 3.120 nonbonded pdb=" O3 NAG B 501 " pdb=" C1 NAG B 502 " model vdw 2.079 3.470 nonbonded pdb=" OE1 GLU B 178 " pdb=" OG SER B 197 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU B 299 " pdb=" OH TYR B 337 " model vdw 2.263 3.040 ... (remaining 40346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 7.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.021 1.439 5295 Z= 1.127 Angle : 1.322 22.502 7222 Z= 0.841 Chirality : 0.073 0.347 782 Planarity : 0.036 0.495 929 Dihedral : 17.141 119.842 1997 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 2.79 % Allowed : 9.92 % Favored : 87.29 % Rotamer: Outliers : 8.03 % Allowed : 12.39 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.12 (0.30), residues: 645 helix: -3.36 (0.40), residues: 69 sheet: -0.95 (0.47), residues: 132 loop : -2.37 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 409 TYR 0.031 0.002 TYR A 501 PHE 0.026 0.002 PHE A 383 TRP 0.030 0.002 TRP B 269 HIS 0.006 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 5276) covalent geometry : angle 1.28280 ( 7183) SS BOND : bond 0.02316 ( 18) SS BOND : angle 2.50735 ( 36) hydrogen bonds : bond 0.25193 ( 105) hydrogen bonds : angle 10.52951 ( 270) link_NAG-ASN : bond 1.43891 ( 1) link_NAG-ASN : angle 13.78990 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.186 Fit side-chains REVERT: A 337 SER cc_start: 0.9441 (m) cc_final: 0.9094 (t) REVERT: A 410 GLN cc_start: 0.7969 (mm110) cc_final: 0.7715 (mt0) REVERT: A 517 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7785 (mtm-85) REVERT: A 538 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9338 (t) REVERT: A 544 GLU cc_start: 0.8893 (mp0) cc_final: 0.8644 (mp0) REVERT: A 552 ASN cc_start: 0.9140 (t0) cc_final: 0.8785 (t0) REVERT: A 581 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8178 (mt) REVERT: A 602 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (t) REVERT: A 604 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 606 ASP cc_start: 0.8625 (m-30) cc_final: 0.8353 (m-30) REVERT: B 268 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8187 (Cg_exo) REVERT: B 463 SER cc_start: 0.8674 (t) cc_final: 0.8391 (p) outliers start: 46 outliers final: 24 residues processed: 150 average time/residue: 0.0742 time to fit residues: 14.5035 Evaluate side-chains 115 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 17 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: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN A 562 HIS A 587 ASN A 598 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.073905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.063324 restraints weight = 13211.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.064888 restraints weight = 8692.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.065518 restraints weight = 5589.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.065804 restraints weight = 4636.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.065891 restraints weight = 4484.870| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5295 Z= 0.167 Angle : 0.804 24.733 7222 Z= 0.374 Chirality : 0.053 0.604 782 Planarity : 0.005 0.058 929 Dihedral : 9.677 57.569 893 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.98 % Favored : 92.71 % Rotamer: Outliers : 4.19 % Allowed : 17.28 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.61 (0.31), residues: 645 helix: -2.53 (0.44), residues: 70 sheet: -1.69 (0.41), residues: 156 loop : -1.64 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 470 TYR 0.022 0.002 TYR A 426 PHE 0.022 0.002 PHE A 577 TRP 0.019 0.002 TRP B 269 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5276) covalent geometry : angle 0.72922 ( 7183) SS BOND : bond 0.00379 ( 18) SS BOND : angle 0.89507 ( 36) hydrogen bonds : bond 0.04325 ( 105) hydrogen bonds : angle 7.38094 ( 270) link_NAG-ASN : bond 0.05555 ( 1) link_NAG-ASN : angle 16.57903 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8380 (m-40) cc_final: 0.8094 (m-40) REVERT: A 502 ARG cc_start: 0.8352 (ptp-170) cc_final: 0.8002 (ptp-170) REVERT: A 544 GLU cc_start: 0.8906 (mp0) cc_final: 0.8629 (mp0) REVERT: A 562 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7593 (m-70) REVERT: A 578 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: B 268 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8347 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8727 (t0) cc_final: 0.8396 (t0) REVERT: B 463 SER cc_start: 0.9014 (t) cc_final: 0.8718 (p) outliers start: 24 outliers final: 14 residues processed: 115 average time/residue: 0.0714 time to fit residues: 10.9177 Evaluate side-chains 90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.074027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.063323 restraints weight = 12990.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.064812 restraints weight = 8582.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.065784 restraints weight = 6089.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.066212 restraints weight = 4509.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.066310 restraints weight = 4425.505| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5295 Z= 0.143 Angle : 0.741 22.446 7222 Z= 0.343 Chirality : 0.053 0.659 782 Planarity : 0.005 0.053 929 Dihedral : 8.519 58.653 862 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.51 % Favored : 93.33 % Rotamer: Outliers : 3.49 % Allowed : 19.55 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.18 (0.31), residues: 645 helix: -1.99 (0.51), residues: 69 sheet: -1.86 (0.41), residues: 148 loop : -1.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.016 0.001 TYR A 426 PHE 0.018 0.002 PHE A 577 TRP 0.015 0.001 TRP B 269 HIS 0.008 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5276) covalent geometry : angle 0.66998 ( 7183) SS BOND : bond 0.00285 ( 18) SS BOND : angle 0.86014 ( 36) hydrogen bonds : bond 0.03594 ( 105) hydrogen bonds : angle 6.86174 ( 270) link_NAG-ASN : bond 0.04245 ( 1) link_NAG-ASN : angle 15.42224 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.216 Fit side-chains REVERT: A 410 GLN cc_start: 0.7625 (mm110) cc_final: 0.7293 (mt0) REVERT: A 413 ASN cc_start: 0.8440 (m-40) cc_final: 0.8207 (m-40) REVERT: A 544 GLU cc_start: 0.8915 (mp0) cc_final: 0.8686 (mp0) REVERT: B 157 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7645 (mt) REVERT: B 268 PRO cc_start: 0.8576 (Cg_endo) cc_final: 0.8283 (Cg_exo) REVERT: B 384 TRP cc_start: 0.8885 (m-90) cc_final: 0.8601 (m-90) REVERT: B 458 ASP cc_start: 0.8687 (t0) cc_final: 0.8354 (t0) REVERT: B 463 SER cc_start: 0.9025 (t) cc_final: 0.8753 (p) REVERT: B 488 MET cc_start: 0.8435 (mmt) cc_final: 0.7273 (mmt) outliers start: 20 outliers final: 13 residues processed: 97 average time/residue: 0.0724 time to fit residues: 9.2919 Evaluate side-chains 88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.074304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.063622 restraints weight = 13072.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.065095 restraints weight = 8630.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.066157 restraints weight = 6078.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.066514 restraints weight = 4445.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.066625 restraints weight = 4387.671| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5295 Z= 0.126 Angle : 0.691 20.941 7222 Z= 0.322 Chirality : 0.052 0.640 782 Planarity : 0.004 0.050 929 Dihedral : 7.305 57.467 853 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.89 % Favored : 93.95 % Rotamer: Outliers : 2.97 % Allowed : 21.12 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.82 (0.32), residues: 645 helix: -1.57 (0.57), residues: 69 sheet: -1.49 (0.44), residues: 135 loop : -1.06 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.016 0.001 TYR A 426 PHE 0.017 0.002 PHE A 577 TRP 0.013 0.001 TRP B 269 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5276) covalent geometry : angle 0.62563 ( 7183) SS BOND : bond 0.00300 ( 18) SS BOND : angle 0.75000 ( 36) hydrogen bonds : bond 0.03134 ( 105) hydrogen bonds : angle 6.53172 ( 270) link_NAG-ASN : bond 0.04065 ( 1) link_NAG-ASN : angle 14.35460 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7624 (mm110) cc_final: 0.7298 (mt0) REVERT: A 413 ASN cc_start: 0.8489 (m-40) cc_final: 0.8217 (m-40) REVERT: A 540 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9272 (p) REVERT: A 544 GLU cc_start: 0.8901 (mp0) cc_final: 0.8648 (mp0) REVERT: B 157 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 268 PRO cc_start: 0.8566 (Cg_endo) cc_final: 0.8250 (Cg_exo) REVERT: B 293 THR cc_start: 0.8653 (t) cc_final: 0.8428 (t) REVERT: B 384 TRP cc_start: 0.8901 (m-90) cc_final: 0.8645 (m-90) REVERT: B 458 ASP cc_start: 0.8664 (t0) cc_final: 0.8389 (t0) REVERT: B 463 SER cc_start: 0.9055 (t) cc_final: 0.8600 (p) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.0783 time to fit residues: 9.6121 Evaluate side-chains 88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.0050 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.074151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.063432 restraints weight = 13211.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.065034 restraints weight = 8690.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.065930 restraints weight = 6163.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.066374 restraints weight = 4558.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.066485 restraints weight = 4445.942| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5295 Z= 0.127 Angle : 0.671 20.232 7222 Z= 0.313 Chirality : 0.052 0.626 782 Planarity : 0.004 0.048 929 Dihedral : 7.399 56.577 853 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.36 % Favored : 93.49 % Rotamer: Outliers : 3.84 % Allowed : 19.72 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.64 (0.32), residues: 645 helix: -0.98 (0.62), residues: 63 sheet: -1.30 (0.43), residues: 142 loop : -1.04 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 470 TYR 0.015 0.001 TYR A 426 PHE 0.018 0.002 PHE B 311 TRP 0.012 0.001 TRP B 269 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5276) covalent geometry : angle 0.60711 ( 7183) SS BOND : bond 0.00284 ( 18) SS BOND : angle 0.74024 ( 36) hydrogen bonds : bond 0.03041 ( 105) hydrogen bonds : angle 6.41470 ( 270) link_NAG-ASN : bond 0.04058 ( 1) link_NAG-ASN : angle 13.92408 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7609 (mm110) cc_final: 0.7250 (mt0) REVERT: A 413 ASN cc_start: 0.8492 (m-40) cc_final: 0.8208 (m-40) REVERT: A 544 GLU cc_start: 0.8929 (mp0) cc_final: 0.8668 (mp0) REVERT: B 157 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7575 (mt) REVERT: B 384 TRP cc_start: 0.8927 (m-90) cc_final: 0.8645 (m-90) REVERT: B 458 ASP cc_start: 0.8696 (t0) cc_final: 0.8363 (t0) REVERT: B 463 SER cc_start: 0.9103 (t) cc_final: 0.8705 (p) outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 0.0705 time to fit residues: 8.6619 Evaluate side-chains 85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.074752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.063977 restraints weight = 13131.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.065568 restraints weight = 8639.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.066513 restraints weight = 6069.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.067002 restraints weight = 4513.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.067086 restraints weight = 4390.211| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5295 Z= 0.116 Angle : 0.636 19.416 7222 Z= 0.301 Chirality : 0.051 0.617 782 Planarity : 0.004 0.046 929 Dihedral : 7.504 59.505 853 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.97 % Allowed : 20.42 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.52 (0.32), residues: 645 helix: -0.83 (0.63), residues: 63 sheet: -1.22 (0.44), residues: 141 loop : -0.96 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 470 TYR 0.014 0.001 TYR A 426 PHE 0.017 0.001 PHE B 311 TRP 0.010 0.001 TRP B 269 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5276) covalent geometry : angle 0.57314 ( 7183) SS BOND : bond 0.00261 ( 18) SS BOND : angle 0.79044 ( 36) hydrogen bonds : bond 0.02924 ( 105) hydrogen bonds : angle 6.34444 ( 270) link_NAG-ASN : bond 0.03931 ( 1) link_NAG-ASN : angle 13.40220 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8458 (m-40) cc_final: 0.8189 (m-40) REVERT: A 544 GLU cc_start: 0.8920 (mp0) cc_final: 0.8655 (mp0) REVERT: B 157 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7545 (mt) REVERT: B 458 ASP cc_start: 0.8682 (t0) cc_final: 0.8378 (t0) REVERT: B 463 SER cc_start: 0.9035 (t) cc_final: 0.8727 (p) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.0761 time to fit residues: 8.9114 Evaluate side-chains 88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.075019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.064290 restraints weight = 13023.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.065852 restraints weight = 8568.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.066931 restraints weight = 6007.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.067085 restraints weight = 4403.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.067242 restraints weight = 4395.101| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5295 Z= 0.119 Angle : 0.638 19.094 7222 Z= 0.302 Chirality : 0.051 0.610 782 Planarity : 0.004 0.045 929 Dihedral : 7.298 56.834 853 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 20.24 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.51 (0.32), residues: 645 helix: -0.76 (0.63), residues: 63 sheet: -1.35 (0.45), residues: 131 loop : -0.94 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 470 TYR 0.013 0.001 TYR A 426 PHE 0.016 0.001 PHE B 311 TRP 0.010 0.001 TRP B 384 HIS 0.002 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5276) covalent geometry : angle 0.57693 ( 7183) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.80232 ( 36) hydrogen bonds : bond 0.02935 ( 105) hydrogen bonds : angle 6.29267 ( 270) link_NAG-ASN : bond 0.03954 ( 1) link_NAG-ASN : angle 13.20242 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8461 (m-40) cc_final: 0.8205 (m-40) REVERT: A 536 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8515 (mmpt) REVERT: A 544 GLU cc_start: 0.8908 (mp0) cc_final: 0.8638 (mp0) REVERT: B 157 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 293 THR cc_start: 0.8648 (t) cc_final: 0.8417 (t) REVERT: B 458 ASP cc_start: 0.8664 (t0) cc_final: 0.8380 (t0) REVERT: B 463 SER cc_start: 0.8991 (t) cc_final: 0.8743 (p) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.0774 time to fit residues: 8.8938 Evaluate side-chains 86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.074963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.064359 restraints weight = 12921.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.065757 restraints weight = 8640.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.066537 restraints weight = 5830.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.067091 restraints weight = 4776.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.067217 restraints weight = 4431.817| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5295 Z= 0.125 Angle : 0.650 18.921 7222 Z= 0.310 Chirality : 0.051 0.600 782 Planarity : 0.004 0.042 929 Dihedral : 6.868 56.465 849 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 20.42 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.49 (0.32), residues: 645 helix: -0.68 (0.64), residues: 63 sheet: -1.30 (0.45), residues: 131 loop : -0.95 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 470 TYR 0.014 0.001 TYR A 426 PHE 0.019 0.001 PHE B 311 TRP 0.010 0.001 TRP B 269 HIS 0.002 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5276) covalent geometry : angle 0.59155 ( 7183) SS BOND : bond 0.00335 ( 18) SS BOND : angle 0.80396 ( 36) hydrogen bonds : bond 0.02897 ( 105) hydrogen bonds : angle 6.25539 ( 270) link_NAG-ASN : bond 0.03988 ( 1) link_NAG-ASN : angle 13.05944 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8378 (mmp80) REVERT: A 413 ASN cc_start: 0.8476 (m-40) cc_final: 0.8210 (m-40) REVERT: A 536 LYS cc_start: 0.8935 (mmpt) cc_final: 0.8525 (mmpt) REVERT: A 544 GLU cc_start: 0.8917 (mp0) cc_final: 0.8621 (mp0) REVERT: B 157 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 270 GLN cc_start: 0.9000 (tp40) cc_final: 0.8106 (tp40) REVERT: B 293 THR cc_start: 0.8615 (t) cc_final: 0.8367 (t) REVERT: B 458 ASP cc_start: 0.8649 (t0) cc_final: 0.8371 (t0) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0635 time to fit residues: 7.2052 Evaluate side-chains 88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 424 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.073951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.063271 restraints weight = 13002.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.064707 restraints weight = 8750.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.065345 restraints weight = 5891.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.066025 restraints weight = 4934.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.066105 restraints weight = 4482.924| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5295 Z= 0.156 Angle : 0.687 19.838 7222 Z= 0.328 Chirality : 0.052 0.611 782 Planarity : 0.004 0.041 929 Dihedral : 7.155 56.378 845 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.62 % Allowed : 20.59 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.52 (0.32), residues: 645 helix: -0.74 (0.63), residues: 63 sheet: -1.12 (0.43), residues: 139 loop : -1.02 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 470 TYR 0.016 0.002 TYR A 426 PHE 0.023 0.002 PHE B 311 TRP 0.011 0.001 TRP B 269 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5276) covalent geometry : angle 0.62641 ( 7183) SS BOND : bond 0.00373 ( 18) SS BOND : angle 0.84645 ( 36) hydrogen bonds : bond 0.03076 ( 105) hydrogen bonds : angle 6.39865 ( 270) link_NAG-ASN : bond 0.04245 ( 1) link_NAG-ASN : angle 13.65927 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 397 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8407 (mmp80) REVERT: A 413 ASN cc_start: 0.8479 (m-40) cc_final: 0.8202 (m-40) REVERT: A 536 LYS cc_start: 0.8952 (mmpt) cc_final: 0.8543 (mmpt) REVERT: A 544 GLU cc_start: 0.8913 (mp0) cc_final: 0.8582 (mp0) REVERT: B 157 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7574 (mt) REVERT: B 270 GLN cc_start: 0.8984 (tp40) cc_final: 0.8097 (tp40) REVERT: B 293 THR cc_start: 0.8643 (t) cc_final: 0.8438 (t) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.0915 time to fit residues: 9.7302 Evaluate side-chains 87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.073632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.062867 restraints weight = 13409.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.064325 restraints weight = 8795.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.064969 restraints weight = 5888.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.065454 restraints weight = 4930.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.065560 restraints weight = 4587.922| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5295 Z= 0.148 Angle : 0.687 19.731 7222 Z= 0.328 Chirality : 0.052 0.610 782 Planarity : 0.004 0.041 929 Dihedral : 7.233 57.663 845 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.27 % Allowed : 21.64 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.54 (0.32), residues: 645 helix: -0.65 (0.64), residues: 63 sheet: -1.10 (0.43), residues: 139 loop : -1.06 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.019 0.002 TYR A 426 PHE 0.019 0.001 PHE B 311 TRP 0.014 0.001 TRP A 332 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5276) covalent geometry : angle 0.62786 ( 7183) SS BOND : bond 0.00349 ( 18) SS BOND : angle 0.81957 ( 36) hydrogen bonds : bond 0.03106 ( 105) hydrogen bonds : angle 6.37621 ( 270) link_NAG-ASN : bond 0.04176 ( 1) link_NAG-ASN : angle 13.58480 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 397 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8433 (mmp80) REVERT: A 413 ASN cc_start: 0.8422 (m-40) cc_final: 0.8148 (m-40) REVERT: A 536 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8506 (mmpt) REVERT: A 544 GLU cc_start: 0.8917 (mp0) cc_final: 0.8561 (mp0) REVERT: B 157 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 270 GLN cc_start: 0.8978 (tp40) cc_final: 0.8112 (tp40) REVERT: B 293 THR cc_start: 0.8629 (t) cc_final: 0.8415 (t) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.0926 time to fit residues: 9.6910 Evaluate side-chains 82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.074803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.064118 restraints weight = 13397.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.065579 restraints weight = 8817.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.066322 restraints weight = 5864.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.066877 restraints weight = 4824.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.066976 restraints weight = 4454.766| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5295 Z= 0.118 Angle : 0.664 18.660 7222 Z= 0.315 Chirality : 0.051 0.595 782 Planarity : 0.004 0.042 929 Dihedral : 6.836 56.633 845 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.44 % Allowed : 21.12 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.48 (0.32), residues: 645 helix: -0.56 (0.65), residues: 63 sheet: -1.16 (0.45), residues: 129 loop : -1.01 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.017 0.001 TYR A 426 PHE 0.016 0.001 PHE B 311 TRP 0.009 0.001 TRP A 332 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5276) covalent geometry : angle 0.60880 ( 7183) SS BOND : bond 0.00278 ( 18) SS BOND : angle 0.77774 ( 36) hydrogen bonds : bond 0.02876 ( 105) hydrogen bonds : angle 6.23201 ( 270) link_NAG-ASN : bond 0.03871 ( 1) link_NAG-ASN : angle 12.87601 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1003.64 seconds wall clock time: 18 minutes 3.02 seconds (1083.02 seconds total)