Starting phenix.real_space_refine on Tue Jun 10 09:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbl_32405/06_2025/7wbl_32405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbl_32405/06_2025/7wbl_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_32405/06_2025/7wbl_32405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbl_32405/06_2025/7wbl_32405.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbl_32405/06_2025/7wbl_32405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbl_32405/06_2025/7wbl_32405.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.53, per 1000 atoms: 0.70 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: 1.46 Conformation dependent library (CDL) restraints added in 826.6 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: 0.60 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: 1.57 Time building geometry restraints manager: 1.75 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: 3467 16.79 - 33.57: 396 33.57 - 50.36: 90 50.36 - 67.14: 29 67.14 - 83.93: 8 Dihedral angle restraints: 3990 sinusoidal: 1664 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 3987 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 : 15.429 83.928 2475 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (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 TRP 0.031 0.001 TRP A 478 HIS 0.003 0.001 HIS A 401 PHE 0.009 0.001 PHE A 308 TYR 0.017 0.001 TYR B 501 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 4) link_NAG-ASN : angle 2.97912 ( 12) hydrogen bonds : bond 0.14089 ( 302) hydrogen bonds : angle 5.84379 ( 846) metal coordination : bond 0.00198 ( 2) SS BOND : bond 0.01108 ( 7) SS BOND : angle 1.91911 ( 14) covalent geometry : bond 0.00385 ( 6667) covalent geometry : angle 0.59533 ( 9063) *********************** 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 : 0.750 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: 0.1597 time to fit residues: 22.1395 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 : 0.757 ------------------------------------------------------------------------------- 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 65 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4166 r_free = 0.4166 target = 0.201420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.164536 restraints weight = 7371.027| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.12 r_work: 0.3546 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6680 Z= 0.112 Angle : 0.513 10.260 9089 Z= 0.263 Chirality : 0.042 0.249 959 Planarity : 0.003 0.034 1170 Dihedral : 5.594 56.682 947 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 7.33 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 787 helix: 1.49 (0.27), residues: 383 sheet: 0.18 (0.73), residues: 46 loop : -0.53 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.010 0.001 PHE A 464 TYR 0.015 0.001 TYR B 501 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 4) link_NAG-ASN : angle 2.56863 ( 12) hydrogen bonds : bond 0.04456 ( 302) hydrogen bonds : angle 4.54661 ( 846) metal coordination : bond 0.00213 ( 2) SS BOND : bond 0.00503 ( 7) SS BOND : angle 1.53522 ( 14) covalent geometry : bond 0.00241 ( 6667) covalent geometry : angle 0.50143 ( 9063) *********************** 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 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.774 Fit side-chains REVERT: A 269 ASP cc_start: 0.7639 (p0) cc_final: 0.7190 (p0) REVERT: A 479 GLU cc_start: 0.6403 (mt-10) cc_final: 0.6066 (mt-10) REVERT: B 472 ILE cc_start: 0.7940 (mp) cc_final: 0.7646 (tp) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.1618 time to fit residues: 22.4470 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 51 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 6 optimal weight: 0.8980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.202107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167862 restraints weight = 7399.202| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.11 r_work: 0.3607 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 6680 Z= 0.096 Angle : 0.476 10.574 9089 Z= 0.242 Chirality : 0.040 0.233 959 Planarity : 0.003 0.031 1170 Dihedral : 4.786 50.211 945 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 0.86 % Allowed : 9.91 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 787 helix: 1.65 (0.27), residues: 387 sheet: 0.59 (0.76), residues: 46 loop : -0.37 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE A 308 TYR 0.015 0.001 TYR A 50 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 1.89466 ( 12) hydrogen bonds : bond 0.03662 ( 302) hydrogen bonds : angle 4.36288 ( 846) metal coordination : bond 0.00105 ( 2) SS BOND : bond 0.01051 ( 7) SS BOND : angle 1.86413 ( 14) covalent geometry : bond 0.00203 ( 6667) covalent geometry : angle 0.46584 ( 9063) *********************** 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: 6 poor density : 98 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 479 GLU cc_start: 0.6392 (mt-10) cc_final: 0.6127 (mt-10) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.1517 time to fit residues: 21.8620 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 0.0010 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4186 r_free = 0.4186 target = 0.203567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168447 restraints weight = 7453.370| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.15 r_work: 0.3594 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 6680 Z= 0.095 Angle : 0.471 11.769 9089 Z= 0.240 Chirality : 0.040 0.219 959 Planarity : 0.003 0.031 1170 Dihedral : 4.395 40.716 945 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.59 % Rotamer: Outliers : 1.44 % Allowed : 11.21 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.30), residues: 787 helix: 1.71 (0.27), residues: 387 sheet: 0.79 (0.77), residues: 45 loop : -0.36 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 PHE 0.007 0.001 PHE A 464 TYR 0.010 0.001 TYR A 50 ARG 0.005 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 4) link_NAG-ASN : angle 1.67158 ( 12) hydrogen bonds : bond 0.03636 ( 302) hydrogen bonds : angle 4.30027 ( 846) metal coordination : bond 0.00135 ( 2) SS BOND : bond 0.00667 ( 7) SS BOND : angle 1.54240 ( 14) covalent geometry : bond 0.00206 ( 6667) covalent geometry : angle 0.46338 ( 9063) *********************** 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 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 293 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6644 (t) REVERT: A 479 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6150 (mt-10) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.1385 time to fit residues: 19.8459 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.0060 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.196204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160338 restraints weight = 7444.938| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.19 r_work: 0.3540 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6680 Z= 0.121 Angle : 0.495 11.714 9089 Z= 0.253 Chirality : 0.041 0.210 959 Planarity : 0.003 0.035 1170 Dihedral : 4.306 30.783 945 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.16 % Allowed : 12.21 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.30), residues: 787 helix: 1.66 (0.27), residues: 385 sheet: 0.68 (0.78), residues: 46 loop : -0.34 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 PHE 0.011 0.001 PHE A 308 TYR 0.012 0.001 TYR B 501 ARG 0.006 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 4) link_NAG-ASN : angle 1.67013 ( 12) hydrogen bonds : bond 0.04167 ( 302) hydrogen bonds : angle 4.34505 ( 846) metal coordination : bond 0.00314 ( 2) SS BOND : bond 0.00687 ( 7) SS BOND : angle 1.52567 ( 14) covalent geometry : bond 0.00278 ( 6667) covalent geometry : angle 0.48814 ( 9063) *********************** 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: 15 poor density : 93 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 293 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6655 (t) REVERT: A 479 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6215 (mt-10) outliers start: 15 outliers final: 9 residues processed: 103 average time/residue: 0.1399 time to fit residues: 20.9238 Evaluate side-chains 101 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 293 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4164 r_free = 0.4164 target = 0.201310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.163470 restraints weight = 7405.169| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.25 r_work: 0.3548 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1430 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= 0.103 Angle : 0.499 11.756 9089 Z= 0.251 Chirality : 0.041 0.200 959 Planarity : 0.003 0.033 1170 Dihedral : 4.105 30.227 945 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.44 % Allowed : 13.07 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.31), residues: 787 helix: 1.57 (0.27), residues: 393 sheet: 0.90 (0.78), residues: 45 loop : -0.33 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.008 0.001 PHE A 308 TYR 0.011 0.001 TYR A 516 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 4) link_NAG-ASN : angle 1.58108 ( 12) hydrogen bonds : bond 0.03844 ( 302) hydrogen bonds : angle 4.31483 ( 846) metal coordination : bond 0.00191 ( 2) SS BOND : bond 0.00874 ( 7) SS BOND : angle 1.79547 ( 14) covalent geometry : bond 0.00232 ( 6667) covalent geometry : angle 0.49114 ( 9063) *********************** 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 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 479 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6280 (mt-10) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.1467 time to fit residues: 20.8307 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.197643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159488 restraints weight = 7413.601| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.99 r_work: 0.3573 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1489 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= 0.107 Angle : 0.507 11.787 9089 Z= 0.256 Chirality : 0.041 0.195 959 Planarity : 0.003 0.033 1170 Dihedral : 4.037 30.258 945 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 13.36 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.31), residues: 787 helix: 1.62 (0.27), residues: 388 sheet: 0.62 (0.71), residues: 55 loop : -0.36 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.010 0.001 PHE A 308 TYR 0.012 0.001 TYR A 516 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 1.57396 ( 12) hydrogen bonds : bond 0.03937 ( 302) hydrogen bonds : angle 4.30355 ( 846) metal coordination : bond 0.00230 ( 2) SS BOND : bond 0.00756 ( 7) SS BOND : angle 1.66133 ( 14) covalent geometry : bond 0.00239 ( 6667) covalent geometry : angle 0.50060 ( 9063) *********************** 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 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.755 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.1554 time to fit residues: 22.0081 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 55 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.202324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164068 restraints weight = 7440.823| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.29 r_work: 0.3560 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1593 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= 0.097 Angle : 0.505 11.726 9089 Z= 0.252 Chirality : 0.041 0.194 959 Planarity : 0.003 0.031 1170 Dihedral : 3.930 29.246 945 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.29 % Allowed : 13.94 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.31), residues: 787 helix: 1.68 (0.27), residues: 390 sheet: 1.10 (0.81), residues: 45 loop : -0.26 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.006 0.001 PHE A 315 TYR 0.011 0.001 TYR A 516 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 1.52859 ( 12) hydrogen bonds : bond 0.03626 ( 302) hydrogen bonds : angle 4.27925 ( 846) metal coordination : bond 0.00147 ( 2) SS BOND : bond 0.00769 ( 7) SS BOND : angle 1.46720 ( 14) covalent geometry : bond 0.00212 ( 6667) covalent geometry : angle 0.49945 ( 9063) *********************** 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: 9 poor density : 91 time to evaluate : 1.618 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.2290 time to fit residues: 32.5273 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.198906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164591 restraints weight = 7504.952| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.89 r_work: 0.3553 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6680 Z= 0.115 Angle : 0.530 11.718 9089 Z= 0.263 Chirality : 0.041 0.191 959 Planarity : 0.003 0.033 1170 Dihedral : 4.050 29.960 945 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 14.22 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.31), residues: 787 helix: 1.66 (0.27), residues: 384 sheet: 0.71 (0.71), residues: 55 loop : -0.32 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 478 HIS 0.005 0.001 HIS A 265 PHE 0.009 0.001 PHE A 308 TYR 0.013 0.001 TYR A 50 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 4) link_NAG-ASN : angle 1.56377 ( 12) hydrogen bonds : bond 0.04059 ( 302) hydrogen bonds : angle 4.31889 ( 846) metal coordination : bond 0.00264 ( 2) SS BOND : bond 0.00757 ( 7) SS BOND : angle 1.55064 ( 14) covalent geometry : bond 0.00259 ( 6667) covalent geometry : angle 0.52396 ( 9063) *********************** 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 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.676 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 91 average time/residue: 0.1730 time to fit residues: 22.5324 Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 5 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.201242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.164392 restraints weight = 7519.834| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.21 r_work: 0.3568 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1671 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= 0.101 Angle : 0.515 11.776 9089 Z= 0.255 Chirality : 0.041 0.191 959 Planarity : 0.003 0.031 1170 Dihedral : 3.942 29.536 945 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 1.44 % Allowed : 14.08 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.31), residues: 787 helix: 1.62 (0.27), residues: 390 sheet: 1.17 (0.81), residues: 45 loop : -0.26 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.008 0.001 PHE A 308 TYR 0.013 0.001 TYR B 423 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 4) link_NAG-ASN : angle 1.53484 ( 12) hydrogen bonds : bond 0.03726 ( 302) hydrogen bonds : angle 4.29073 ( 846) metal coordination : bond 0.00188 ( 2) SS BOND : bond 0.00742 ( 7) SS BOND : angle 1.53313 ( 14) covalent geometry : bond 0.00224 ( 6667) covalent geometry : angle 0.50938 ( 9063) ********************** 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 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.5872 (mm-30) cc_final: 0.5309 (mt-10) outliers start: 10 outliers final: 10 residues processed: 91 average time/residue: 0.2125 time to fit residues: 28.5385 Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.198477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163571 restraints weight = 7579.558| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.04 r_work: 0.3563 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1703 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 : 0.512 11.729 9089 Z= 0.254 Chirality : 0.041 0.190 959 Planarity : 0.003 0.031 1170 Dihedral : 3.913 29.294 945 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.44 % Allowed : 14.22 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.31), residues: 787 helix: 1.62 (0.27), residues: 390 sheet: 1.23 (0.82), residues: 45 loop : -0.26 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 PHE 0.008 0.001 PHE A 308 TYR 0.012 0.001 TYR A 50 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 1.52652 ( 12) hydrogen bonds : bond 0.03788 ( 302) hydrogen bonds : angle 4.28149 ( 846) metal coordination : bond 0.00201 ( 2) SS BOND : bond 0.00743 ( 7) SS BOND : angle 1.54340 ( 14) covalent geometry : bond 0.00229 ( 6667) covalent geometry : angle 0.50647 ( 9063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4532.68 seconds wall clock time: 82 minutes 31.67 seconds (4951.67 seconds total)