Starting phenix.real_space_refine on Fri Jul 3 02:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbl_32405/07_2026/7wbl_32405.cif" } resolution = 3.4 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6402 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4152 2.51 5 N 1073 2.21 5 O 1221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.44, per 1000 atoms: 0.22 Number of scatterers: 6484 At special positions: 0 Unit cell: (75.71, 86.43, 123.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1221 8.00 N 1073 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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 801 " - " ASN A 103 " " NAG A 802 " - " ASN A 53 " " NAG A 803 " - " ASN A 90 " " NAG A 804 " - " ASN A 322 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 362.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 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: 39 helices and 5 sheets defined 56.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.952A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.588A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.092A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.690A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.576A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.545A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.684A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.818A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.820A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.579A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.710A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.525A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.051A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.633A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.733A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.938A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.816A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.893A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.563A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.143A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.299A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.563A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 302 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: 0.77 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.48: 1774 1.48 - 1.61: 2741 1.61 - 1.74: 0 1.74 - 1.87: 58 Bond restraints: 6667 Sorted by residual: bond pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.36e+01 bond pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta sigma weight residual 1.448 1.475 -0.027 9.00e-03 1.23e+04 8.81e+00 bond pdb=" N ARG B 498 " pdb=" CA ARG B 498 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.50e-02 4.44e+03 7.56e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.19e-02 7.06e+03 6.98e+00 bond pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.30e+00 ... (remaining 6662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 8969 2.49 - 4.97: 82 4.97 - 7.46: 7 7.46 - 9.94: 3 9.94 - 12.43: 2 Bond angle restraints: 9063 Sorted by residual: angle pdb=" C ARG B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.84 132.27 -12.43 1.25e+00 6.40e-01 9.88e+01 angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" O GLY A 352 " ideal model delta sigma weight residual 122.45 118.18 4.27 7.20e-01 1.93e+00 3.51e+01 angle pdb=" CA ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 117.93 126.11 -8.18 1.42e+00 4.96e-01 3.32e+01 angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 126.48 -12.08 2.30e+00 1.89e-01 2.76e+01 angle pdb=" O ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 121.72 117.79 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 9058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3397 16.79 - 33.57: 390 33.57 - 50.36: 86 50.36 - 67.14: 25 67.14 - 83.93: 8 Dihedral angle restraints: 3906 sinusoidal: 1580 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 45.60 47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 56.80 36.20 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -114.71 28.71 1 1.00e+01 1.00e-02 1.18e+01 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 798 0.055 - 0.110: 141 0.110 - 0.164: 17 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ARG B 498 " pdb=" N ARG B 498 " pdb=" C ARG B 498 " pdb=" CB ARG B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 956 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 497 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C PHE B 497 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE B 497 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG B 498 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.013 2.00e-02 2.50e+03 1.17e-02 3.44e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 156 2.71 - 3.26: 6280 3.26 - 3.80: 9928 3.80 - 4.35: 12420 4.35 - 4.90: 21633 Nonbonded interactions: 50417 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 805 " model vdw 2.158 2.230 nonbonded pdb=" O SER B 496 " pdb=" OH TYR B 501 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.235 3.040 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.302 3.120 ... (remaining 50412 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.004 0.171 6680 Z= 0.208 Angle : 0.609 12.427 9089 Z= 0.344 Chirality : 0.044 0.274 959 Planarity : 0.004 0.040 1170 Dihedral : 15.354 83.928 2391 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.56 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 0.86 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.52 (0.30), residues: 787 helix: 1.27 (0.27), residues: 379 sheet: 0.20 (0.74), residues: 46 loop : -0.59 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.017 0.001 TYR B 501 PHE 0.009 0.001 PHE A 308 TRP 0.031 0.001 TRP A 478 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.21 ( 6667) covalent geometry : angle 0.59533 / 0.34 ( 9063) SS BOND : bond 0.01108 / 0.86 ( 7) SS BOND : angle 1.91911 / 1.19 ( 14) hydrogen bonds : bond 0.14089 / 9.50 ( 302) hydrogen bonds : angle 5.84379 / 4.12 ( 846) metal coordination : bond 0.00198 / 0.10 ( 2) link_NAG-ASN : bond 0.00729 / 0.36 ( 4) link_NAG-ASN : angle 2.97912 / 2.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.247 Fit side-chains REVERT: A 159 ASN cc_start: 0.6522 (m-40) cc_final: 0.6261 (m-40) REVERT: A 269 ASP cc_start: 0.7718 (p0) cc_final: 0.7295 (p0) REVERT: B 472 ILE cc_start: 0.7817 (mp) cc_final: 0.7548 (tp) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.0648 time to fit residues: 9.2022 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.194796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155943 restraints weight = 7579.914| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.17 r_work: 0.3527 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6680 Z= 0.134 Angle : 0.534 10.407 9089 Z= 0.275 Chirality : 0.043 0.258 959 Planarity : 0.004 0.039 1170 Dihedral : 3.993 27.690 863 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.44 % Allowed : 8.33 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.58 (0.30), residues: 787 helix: 1.34 (0.27), residues: 383 sheet: 0.11 (0.73), residues: 46 loop : -0.60 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.020 0.002 TYR B 501 PHE 0.011 0.001 PHE A 308 TRP 0.019 0.001 TRP A 478 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6667) covalent geometry : angle 0.52337 / 0.27 ( 9063) SS BOND : bond 0.00562 / 0.42 ( 7) SS BOND : angle 1.55276 / 0.96 ( 14) hydrogen bonds : bond 0.04916 / 3.28 ( 302) hydrogen bonds : angle 4.61019 / 3.24 ( 846) metal coordination : bond 0.00332 / 0.16 ( 2) link_NAG-ASN : bond 0.00646 / 0.32 ( 4) link_NAG-ASN : angle 2.56584 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.157 Fit side-chains REVERT: A 269 ASP cc_start: 0.7725 (p0) cc_final: 0.7459 (p0) REVERT: B 472 ILE cc_start: 0.7957 (mp) cc_final: 0.7648 (tp) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.0609 time to fit residues: 8.1583 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 45 optimal weight: 0.0010 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.196344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159239 restraints weight = 7435.476| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.06 r_work: 0.3528 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6680 Z= 0.110 Angle : 0.502 11.278 9089 Z= 0.256 Chirality : 0.041 0.231 959 Planarity : 0.003 0.036 1170 Dihedral : 3.733 15.095 861 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 1.15 % Allowed : 10.20 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.80 (0.30), residues: 787 helix: 1.53 (0.27), residues: 379 sheet: 0.11 (0.68), residues: 56 loop : -0.46 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.014 0.001 TYR A 50 PHE 0.011 0.001 PHE A 308 TRP 0.017 0.001 TRP A 478 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6667) covalent geometry : angle 0.49344 / 0.25 ( 9063) SS BOND : bond 0.00759 / 0.58 ( 7) SS BOND : angle 1.63242 / 1.10 ( 14) hydrogen bonds : bond 0.04234 / 2.85 ( 302) hydrogen bonds : angle 4.45496 / 3.13 ( 846) metal coordination : bond 0.00208 / 0.10 ( 2) link_NAG-ASN : bond 0.00513 / 0.26 ( 4) link_NAG-ASN : angle 1.93759 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.204 Fit side-chains REVERT: A 269 ASP cc_start: 0.7595 (p0) cc_final: 0.7139 (p0) REVERT: B 472 ILE cc_start: 0.7982 (mp) cc_final: 0.7702 (tp) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.0532 time to fit residues: 7.7088 Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 194 ASN A 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.195470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.157118 restraints weight = 7570.580| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.17 r_work: 0.3515 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6680 Z= 0.123 Angle : 0.506 11.960 9089 Z= 0.260 Chirality : 0.041 0.211 959 Planarity : 0.004 0.036 1170 Dihedral : 3.778 15.057 861 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 10.92 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.79 (0.30), residues: 787 helix: 1.50 (0.27), residues: 382 sheet: 0.16 (0.68), residues: 56 loop : -0.47 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 482 TYR 0.010 0.001 TYR A 50 PHE 0.011 0.001 PHE A 308 TRP 0.014 0.001 TRP A 478 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6667) covalent geometry : angle 0.49853 / 0.26 ( 9063) SS BOND : bond 0.00713 / 0.54 ( 7) SS BOND : angle 1.60577 / 1.06 ( 14) hydrogen bonds : bond 0.04436 / 2.98 ( 302) hydrogen bonds : angle 4.41687 / 3.10 ( 846) metal coordination : bond 0.00311 / 0.15 ( 2) link_NAG-ASN : bond 0.00430 / 0.21 ( 4) link_NAG-ASN : angle 1.71109 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7645 (p0) cc_final: 0.7358 (p0) REVERT: A 293 VAL cc_start: 0.6921 (OUTLIER) cc_final: 0.6688 (t) REVERT: B 472 ILE cc_start: 0.8000 (mp) cc_final: 0.7709 (tp) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.0673 time to fit residues: 9.7507 Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.189739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.150048 restraints weight = 7628.790| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.30 r_work: 0.3460 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6680 Z= 0.185 Angle : 0.569 12.095 9089 Z= 0.295 Chirality : 0.044 0.200 959 Planarity : 0.004 0.040 1170 Dihedral : 4.087 15.630 861 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 2.30 % Allowed : 11.78 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.56 (0.30), residues: 787 helix: 1.31 (0.26), residues: 376 sheet: 0.12 (0.67), residues: 56 loop : -0.56 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.014 0.002 TYR A 587 PHE 0.017 0.002 PHE A 308 TRP 0.017 0.002 TRP A 478 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 6667) covalent geometry : angle 0.56190 / 0.29 ( 9063) SS BOND : bond 0.00718 / 0.54 ( 7) SS BOND : angle 1.62150 / 1.05 ( 14) hydrogen bonds : bond 0.05350 / 3.60 ( 302) hydrogen bonds : angle 4.58078 / 3.23 ( 846) metal coordination : bond 0.00611 / 0.30 ( 2) link_NAG-ASN : bond 0.00465 / 0.23 ( 4) link_NAG-ASN : angle 1.80931 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.6976 (m-40) cc_final: 0.6572 (m-40) REVERT: A 293 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6850 (t) REVERT: B 442 ASP cc_start: 0.7608 (m-30) cc_final: 0.7181 (t0) REVERT: B 472 ILE cc_start: 0.8044 (mp) cc_final: 0.7734 (tp) outliers start: 16 outliers final: 14 residues processed: 103 average time/residue: 0.0716 time to fit residues: 10.3820 Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.195297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.157429 restraints weight = 7525.558| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.24 r_work: 0.3523 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 6680 Z= 0.109 Angle : 0.509 11.987 9089 Z= 0.260 Chirality : 0.041 0.192 959 Planarity : 0.004 0.035 1170 Dihedral : 3.828 15.278 861 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 12.79 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.84 (0.30), residues: 787 helix: 1.57 (0.27), residues: 376 sheet: 0.26 (0.69), residues: 56 loop : -0.46 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.019 0.001 TYR A 515 PHE 0.009 0.001 PHE B 347 TRP 0.021 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6667) covalent geometry : angle 0.50200 / 0.26 ( 9063) SS BOND : bond 0.00866 / 0.59 ( 7) SS BOND : angle 1.71321 / 1.08 ( 14) hydrogen bonds : bond 0.04138 / 2.78 ( 302) hydrogen bonds : angle 4.39635 / 3.08 ( 846) metal coordination : bond 0.00244 / 0.12 ( 2) link_NAG-ASN : bond 0.00360 / 0.18 ( 4) link_NAG-ASN : angle 1.51463 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7532 (p0) cc_final: 0.7084 (p0) REVERT: A 293 VAL cc_start: 0.6935 (OUTLIER) cc_final: 0.6720 (t) REVERT: B 442 ASP cc_start: 0.7587 (m-30) cc_final: 0.7161 (t0) REVERT: B 472 ILE cc_start: 0.8007 (mp) cc_final: 0.7723 (tp) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.0615 time to fit residues: 8.7961 Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.197165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158792 restraints weight = 7448.171| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.24 r_work: 0.3529 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6680 Z= 0.103 Angle : 0.507 11.782 9089 Z= 0.255 Chirality : 0.041 0.191 959 Planarity : 0.003 0.032 1170 Dihedral : 3.739 20.996 861 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 13.94 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 787 helix: 1.66 (0.27), residues: 378 sheet: 0.46 (0.71), residues: 56 loop : -0.39 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.015 0.001 TYR A 515 PHE 0.010 0.001 PHE A 308 TRP 0.023 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6667) covalent geometry : angle 0.50127 / 0.25 ( 9063) SS BOND : bond 0.00775 / 0.54 ( 7) SS BOND : angle 1.55029 / 0.99 ( 14) hydrogen bonds : bond 0.03960 / 2.65 ( 302) hydrogen bonds : angle 4.32618 / 3.02 ( 846) metal coordination : bond 0.00220 / 0.11 ( 2) link_NAG-ASN : bond 0.00348 / 0.17 ( 4) link_NAG-ASN : angle 1.44189 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7474 (p0) cc_final: 0.7008 (p0) REVERT: A 293 VAL cc_start: 0.6937 (OUTLIER) cc_final: 0.6732 (t) REVERT: B 442 ASP cc_start: 0.7622 (m-30) cc_final: 0.7185 (t0) REVERT: B 472 ILE cc_start: 0.8002 (mp) cc_final: 0.7723 (tp) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.0552 time to fit residues: 8.1062 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.196287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.158066 restraints weight = 7502.570| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.12 r_work: 0.3520 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6680 Z= 0.105 Angle : 0.509 11.752 9089 Z= 0.255 Chirality : 0.041 0.189 959 Planarity : 0.003 0.032 1170 Dihedral : 3.719 21.214 861 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.72 % Allowed : 14.51 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 1.03 (0.31), residues: 787 helix: 1.70 (0.27), residues: 378 sheet: 0.50 (0.71), residues: 56 loop : -0.37 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.013 0.001 TYR A 515 PHE 0.009 0.001 PHE A 308 TRP 0.022 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6667) covalent geometry : angle 0.50352 / 0.25 ( 9063) SS BOND : bond 0.00752 / 0.53 ( 7) SS BOND : angle 1.57077 / 1.00 ( 14) hydrogen bonds : bond 0.03921 / 2.63 ( 302) hydrogen bonds : angle 4.30857 / 3.02 ( 846) metal coordination : bond 0.00221 / 0.11 ( 2) link_NAG-ASN : bond 0.00339 / 0.17 ( 4) link_NAG-ASN : angle 1.41412 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7454 (p0) cc_final: 0.6996 (p0) REVERT: B 442 ASP cc_start: 0.7611 (m-30) cc_final: 0.7178 (t0) REVERT: B 472 ILE cc_start: 0.7999 (mp) cc_final: 0.7729 (tp) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.0573 time to fit residues: 7.9974 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 67 optimal weight: 0.0050 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.195785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.157119 restraints weight = 7613.045| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.27 r_work: 0.3515 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6680 Z= 0.109 Angle : 0.515 11.752 9089 Z= 0.259 Chirality : 0.041 0.186 959 Planarity : 0.003 0.033 1170 Dihedral : 3.739 20.775 861 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.58 % Allowed : 15.09 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 1.02 (0.31), residues: 787 helix: 1.62 (0.27), residues: 384 sheet: 0.51 (0.72), residues: 56 loop : -0.31 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.013 0.001 TYR A 515 PHE 0.010 0.001 PHE A 308 TRP 0.021 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6667) covalent geometry : angle 0.50925 / 0.26 ( 9063) SS BOND : bond 0.00740 / 0.53 ( 7) SS BOND : angle 1.58916 / 1.01 ( 14) hydrogen bonds : bond 0.03990 / 2.68 ( 302) hydrogen bonds : angle 4.30442 / 3.01 ( 846) metal coordination : bond 0.00248 / 0.12 ( 2) link_NAG-ASN : bond 0.00338 / 0.17 ( 4) link_NAG-ASN : angle 1.41195 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 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: 11 poor density : 87 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7468 (p0) cc_final: 0.6990 (p0) REVERT: B 442 ASP cc_start: 0.7633 (m-30) cc_final: 0.7193 (t0) REVERT: B 472 ILE cc_start: 0.8006 (mp) cc_final: 0.7730 (tp) outliers start: 11 outliers final: 11 residues processed: 94 average time/residue: 0.0562 time to fit residues: 7.7301 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.199954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162106 restraints weight = 7433.595| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.17 r_work: 0.3556 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 6680 Z= 0.253 Angle : 0.503 11.784 9089 Z= 0.252 Chirality : 0.040 0.186 959 Planarity : 0.003 0.030 1170 Dihedral : 3.643 20.016 861 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.72 % Allowed : 15.09 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 1.14 (0.31), residues: 787 helix: 1.73 (0.27), residues: 384 sheet: 0.65 (0.73), residues: 56 loop : -0.28 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.013 0.001 TYR B 423 PHE 0.007 0.001 PHE A 315 TRP 0.024 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 6667) covalent geometry : angle 0.49806 / 0.25 ( 9063) SS BOND : bond 0.00735 / 0.53 ( 7) SS BOND : angle 1.53648 / 0.97 ( 14) hydrogen bonds : bond 0.03585 / 2.40 ( 302) hydrogen bonds : angle 4.25563 / 2.97 ( 846) metal coordination : bond 0.40531 / 21.33 ( 2) link_NAG-ASN : bond 0.00318 / 0.16 ( 4) link_NAG-ASN : angle 1.35173 / 0.83 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5316 (mt-10) REVERT: B 442 ASP cc_start: 0.7590 (m-30) cc_final: 0.7161 (t0) REVERT: B 472 ILE cc_start: 0.7984 (mp) cc_final: 0.7743 (tp) outliers start: 12 outliers final: 11 residues processed: 98 average time/residue: 0.0543 time to fit residues: 7.7914 Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.0060 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.199318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.161348 restraints weight = 7579.633| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.28 r_work: 0.3549 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6680 Z= 0.100 Angle : 0.510 11.710 9089 Z= 0.255 Chirality : 0.040 0.184 959 Planarity : 0.003 0.030 1170 Dihedral : 3.639 19.209 861 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 15.09 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 1.18 (0.31), residues: 787 helix: 1.74 (0.27), residues: 384 sheet: 1.22 (0.84), residues: 46 loop : -0.30 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.012 0.001 TYR A 515 PHE 0.007 0.001 PHE A 315 TRP 0.029 0.001 TRP A 302 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 6667) covalent geometry : angle 0.50472 / 0.25 ( 9063) SS BOND : bond 0.00717 / 0.51 ( 7) SS BOND : angle 1.53613 / 0.97 ( 14) hydrogen bonds : bond 0.03618 / 2.41 ( 302) hydrogen bonds : angle 4.25533 / 2.98 ( 846) metal coordination : bond 0.00392 / 0.19 ( 2) link_NAG-ASN : bond 0.00310 / 0.15 ( 4) link_NAG-ASN : angle 1.33312 / 0.81 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.60 seconds wall clock time: 26 minutes 34.45 seconds (1594.45 seconds total)