Starting phenix.real_space_refine on Wed May 14 07:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.map" model { file = "/net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we0_37469/05_2025/8we0_37469.cif" } resolution = 2.8 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= 0.001 sd= 0.027 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 6315 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 4182 2.51 5 N 1074 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6538 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.18, per 1000 atoms: 0.95 Number of scatterers: 6538 At special positions: 0 Unit cell: (75.65, 85.85, 124.1, 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 1244 8.00 N 1074 7.00 C 4182 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=2.05 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=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 546 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 906 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 49.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.844A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.852A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.680A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.951A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.593A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.606A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.639A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 4.396A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.591A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.663A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.556A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 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: 3.734A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.560A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.710A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.817A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.555A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.277A pdb=" N ILE B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.491A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.515A 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: 6.190A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.672A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 245 hydrogen bonds defined for protein. 696 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: 1.49 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1082 1.32 - 1.44: 1963 1.44 - 1.57: 3621 1.57 - 1.69: 0 1.69 - 1.82: 58 Bond restraints: 6724 Sorted by residual: bond pdb=" N ASN B 422 " pdb=" CA ASN B 422 " ideal model delta sigma weight residual 1.458 1.490 -0.031 6.30e-03 2.52e+04 2.45e+01 bond pdb=" CE1 HIS B 339 " pdb=" NE2 HIS B 339 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.53e+01 bond pdb=" CE1 HIS A 195 " pdb=" NE2 HIS A 195 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.48e+01 bond pdb=" C PRO A 583 " pdb=" O PRO A 583 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.29e-02 6.01e+03 1.40e+01 bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.532 1.473 0.059 1.58e-02 4.01e+03 1.38e+01 ... (remaining 6719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 8578 2.37 - 4.73: 480 4.73 - 7.10: 69 7.10 - 9.46: 11 9.46 - 11.83: 6 Bond angle restraints: 9144 Sorted by residual: angle pdb=" N GLU B 340 " pdb=" CA GLU B 340 " pdb=" C GLU B 340 " ideal model delta sigma weight residual 113.88 104.08 9.80 1.23e+00 6.61e-01 6.35e+01 angle pdb=" N PRO A 321 " pdb=" CA PRO A 321 " pdb=" C PRO A 321 " ideal model delta sigma weight residual 110.40 122.23 -11.83 1.61e+00 3.86e-01 5.39e+01 angle pdb=" N LYS A 475 " pdb=" CA LYS A 475 " pdb=" C LYS A 475 " ideal model delta sigma weight residual 113.12 104.52 8.60 1.25e+00 6.40e-01 4.73e+01 angle pdb=" C ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta sigma weight residual 111.83 101.38 10.45 1.60e+00 3.91e-01 4.26e+01 angle pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" O GLY A 605 " ideal model delta sigma weight residual 122.37 117.67 4.70 7.30e-01 1.88e+00 4.15e+01 ... (remaining 9139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 3781 26.41 - 52.83: 252 52.83 - 79.24: 42 79.24 - 105.65: 9 105.65 - 132.06: 1 Dihedral angle restraints: 4085 sinusoidal: 1757 harmonic: 2328 Sorted by residual: dihedral pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " pdb=" CZ ARG B 355 " pdb=" NH1 ARG B 355 " ideal model delta sinusoidal sigma weight residual 0.00 -77.86 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " pdb=" NH1 ARG B 357 " ideal model delta sinusoidal sigma weight residual 0.00 -73.16 73.16 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CD ARG A 582 " pdb=" NE ARG A 582 " pdb=" CZ ARG A 582 " pdb=" NH1 ARG A 582 " ideal model delta sinusoidal sigma weight residual 0.00 -48.23 48.23 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 4082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.911: 979 0.911 - 1.821: 0 1.821 - 2.732: 0 2.732 - 3.643: 0 3.643 - 4.554: 3 Chirality restraints: 982 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 2.15 -4.55 2.00e-01 2.50e+01 5.18e+02 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 1.61 -4.01 2.00e-01 2.50e+01 4.02e+02 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 1.36 -3.76 2.00e-01 2.50e+01 3.54e+02 ... (remaining 979 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.311 2.00e-02 2.50e+03 2.70e-01 9.09e+02 pdb=" C7 NAG B 601 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 905 " -0.311 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG A 905 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 905 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 905 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG A 905 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.307 2.00e-02 2.50e+03 2.62e-01 8.57e+02 pdb=" C7 NAG A 902 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.458 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " 0.053 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 5502 3.16 - 3.74: 10134 3.74 - 4.32: 13916 4.32 - 4.90: 22576 Nonbonded interactions: 52195 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 906 " model vdw 2.000 2.230 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.220 3.120 nonbonded pdb=" O ASP A 597 " pdb=" NZ LYS A 600 " model vdw 2.222 3.120 nonbonded pdb=" NH1 ARG A 192 " pdb=" O GLU A 197 " model vdw 2.274 3.120 ... (remaining 52190 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=0.50 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.890 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.008 0.209 6742 Z= 0.499 Angle : 1.173 11.825 9185 Z= 0.762 Chirality : 0.238 4.554 982 Planarity : 0.029 0.480 1173 Dihedral : 17.154 132.065 2570 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 3.30 % Allowed : 10.04 % Favored : 86.66 % Rotamer: Outliers : 8.20 % Allowed : 6.76 % Favored : 85.04 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 2.50 % 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: -1.66 (0.31), residues: 788 helix: -0.06 (0.29), residues: 355 sheet: -0.31 (0.90), residues: 37 loop : -2.22 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 353 HIS 0.006 0.001 HIS A 378 PHE 0.016 0.001 PHE A 314 TYR 0.028 0.002 TYR B 473 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 7) link_NAG-ASN : angle 4.55697 ( 21) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 0.61960 ( 3) hydrogen bonds : bond 0.21108 ( 245) hydrogen bonds : angle 7.57961 ( 696) link_BETA1-6 : bond 0.00198 ( 1) link_BETA1-6 : angle 1.22596 ( 3) metal coordination : bond 0.20583 ( 2) SS BOND : bond 0.01269 ( 7) SS BOND : angle 1.60332 ( 14) covalent geometry : bond 0.00685 ( 6724) covalent geometry : angle 1.15323 ( 9144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 189 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7072 (tp30) REVERT: A 291 ILE cc_start: 0.8427 (mt) cc_final: 0.8207 (mp) REVERT: A 324 THR cc_start: 0.7713 (p) cc_final: 0.7484 (p) REVERT: A 331 SER cc_start: 0.8187 (t) cc_final: 0.7833 (p) REVERT: B 383 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 513 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7318 (mt) outliers start: 57 outliers final: 27 residues processed: 224 average time/residue: 1.0075 time to fit residues: 238.2506 Evaluate side-chains 194 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 GLN A 139 GLN A 149 ASN A 330 ASN A 340 GLN A 493 HIS B 339 HIS B 422 ASN B 439 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130666 restraints weight = 16616.789| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.00 r_work: 0.3577 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6742 Z= 0.147 Angle : 0.801 11.579 9185 Z= 0.382 Chirality : 0.052 0.610 982 Planarity : 0.007 0.107 1173 Dihedral : 9.468 58.023 1114 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.26 % Favored : 91.23 % Rotamer: Outliers : 5.32 % Allowed : 16.83 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.23 (0.30), residues: 788 helix: 0.25 (0.28), residues: 384 sheet: -0.57 (0.87), residues: 41 loop : -2.06 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.027 0.002 PHE A 592 TYR 0.014 0.002 TYR B 351 ARG 0.011 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 7) link_NAG-ASN : angle 5.63124 ( 21) link_BETA1-4 : bond 0.00800 ( 1) link_BETA1-4 : angle 1.47823 ( 3) hydrogen bonds : bond 0.04647 ( 245) hydrogen bonds : angle 4.95228 ( 696) link_BETA1-6 : bond 0.00314 ( 1) link_BETA1-6 : angle 1.43658 ( 3) metal coordination : bond 0.00198 ( 2) SS BOND : bond 0.00376 ( 7) SS BOND : angle 1.12636 ( 14) covalent geometry : bond 0.00324 ( 6724) covalent geometry : angle 0.75343 ( 9144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7346 (tp30) REVERT: A 227 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 407 ILE cc_start: 0.7517 (pt) cc_final: 0.7304 (pt) REVERT: A 468 ILE cc_start: 0.8452 (mt) cc_final: 0.8084 (tt) REVERT: A 470 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: B 357 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5929 (tmm-80) outliers start: 37 outliers final: 17 residues processed: 182 average time/residue: 1.0353 time to fit residues: 199.1953 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS A 580 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.149265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126284 restraints weight = 21774.197| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.40 r_work: 0.3501 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6742 Z= 0.151 Angle : 0.713 11.612 9185 Z= 0.345 Chirality : 0.046 0.359 982 Planarity : 0.006 0.081 1173 Dihedral : 7.839 57.121 1075 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.13 % Favored : 91.61 % Rotamer: Outliers : 4.60 % Allowed : 19.14 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.91 (0.30), residues: 788 helix: 0.45 (0.28), residues: 376 sheet: -0.62 (0.81), residues: 42 loop : -1.74 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 353 HIS 0.005 0.001 HIS A 505 PHE 0.021 0.002 PHE A 592 TYR 0.014 0.002 TYR A 613 ARG 0.013 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 7) link_NAG-ASN : angle 4.14368 ( 21) link_BETA1-4 : bond 0.00264 ( 1) link_BETA1-4 : angle 1.40118 ( 3) hydrogen bonds : bond 0.04573 ( 245) hydrogen bonds : angle 4.63921 ( 696) link_BETA1-6 : bond 0.00419 ( 1) link_BETA1-6 : angle 1.03375 ( 3) metal coordination : bond 0.00658 ( 2) SS BOND : bond 0.00440 ( 7) SS BOND : angle 1.00062 ( 14) covalent geometry : bond 0.00345 ( 6724) covalent geometry : angle 0.68427 ( 9144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 189 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7478 (tp30) REVERT: A 227 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 283 VAL cc_start: 0.8620 (p) cc_final: 0.8387 (t) REVERT: A 318 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 407 ILE cc_start: 0.7461 (pt) cc_final: 0.7257 (pt) REVERT: A 470 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8087 (mtpp) REVERT: A 499 ASP cc_start: 0.7858 (m-30) cc_final: 0.7590 (m-30) REVERT: B 339 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7711 (t70) REVERT: B 347 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: B 357 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5934 (tmm-80) REVERT: B 509 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7987 (mtt90) outliers start: 32 outliers final: 17 residues processed: 176 average time/residue: 1.0596 time to fit residues: 197.0013 Evaluate side-chains 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS B 439 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128265 restraints weight = 11322.173| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.29 r_work: 0.3581 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6742 Z= 0.151 Angle : 0.678 9.924 9185 Z= 0.331 Chirality : 0.046 0.429 982 Planarity : 0.006 0.075 1173 Dihedral : 7.450 57.526 1070 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.75 % Favored : 91.99 % Rotamer: Outliers : 5.47 % Allowed : 19.28 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.67 (0.30), residues: 788 helix: 0.61 (0.28), residues: 371 sheet: -0.63 (0.77), residues: 42 loop : -1.52 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS A 241 PHE 0.015 0.002 PHE A 512 TYR 0.014 0.002 TYR A 215 ARG 0.012 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.01066 ( 7) link_NAG-ASN : angle 4.13644 ( 21) link_BETA1-4 : bond 0.00560 ( 1) link_BETA1-4 : angle 1.23738 ( 3) hydrogen bonds : bond 0.04334 ( 245) hydrogen bonds : angle 4.44055 ( 696) link_BETA1-6 : bond 0.00390 ( 1) link_BETA1-6 : angle 1.13360 ( 3) metal coordination : bond 0.00600 ( 2) SS BOND : bond 0.00446 ( 7) SS BOND : angle 0.89862 ( 14) covalent geometry : bond 0.00349 ( 6724) covalent geometry : angle 0.64854 ( 9144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7953 (t80) cc_final: 0.7708 (t80) REVERT: A 68 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7998 (mtpp) REVERT: A 189 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7655 (tp30) REVERT: A 227 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: A 283 VAL cc_start: 0.8692 (p) cc_final: 0.8476 (t) REVERT: A 288 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7982 (tttt) REVERT: A 318 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 333 LEU cc_start: 0.8918 (mp) cc_final: 0.8706 (mt) REVERT: A 470 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8176 (mtpp) REVERT: B 339 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7788 (t70) REVERT: B 347 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: B 509 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8078 (mtt90) outliers start: 38 outliers final: 22 residues processed: 174 average time/residue: 1.0726 time to fit residues: 196.7742 Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 39 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 137 ASN A 139 GLN A 149 ASN A 195 HIS B 409 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126969 restraints weight = 10198.532| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.16 r_work: 0.3549 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6742 Z= 0.190 Angle : 0.699 9.830 9185 Z= 0.343 Chirality : 0.047 0.371 982 Planarity : 0.006 0.067 1173 Dihedral : 7.168 56.562 1068 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.75 % Favored : 91.99 % Rotamer: Outliers : 5.18 % Allowed : 20.58 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.62 (0.30), residues: 788 helix: 0.64 (0.28), residues: 371 sheet: -0.47 (0.73), residues: 41 loop : -1.51 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS A 505 PHE 0.022 0.002 PHE A 592 TYR 0.016 0.002 TYR A 385 ARG 0.012 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 7) link_NAG-ASN : angle 3.98211 ( 21) link_BETA1-4 : bond 0.00476 ( 1) link_BETA1-4 : angle 1.21006 ( 3) hydrogen bonds : bond 0.04888 ( 245) hydrogen bonds : angle 4.54565 ( 696) link_BETA1-6 : bond 0.00262 ( 1) link_BETA1-6 : angle 0.98551 ( 3) metal coordination : bond 0.00894 ( 2) SS BOND : bond 0.00781 ( 7) SS BOND : angle 0.89544 ( 14) covalent geometry : bond 0.00444 ( 6724) covalent geometry : angle 0.67227 ( 9144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8015 (mtpp) REVERT: A 75 GLU cc_start: 0.7504 (tp30) cc_final: 0.7255 (tp30) REVERT: A 156 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 167 SER cc_start: 0.8480 (m) cc_final: 0.8264 (p) REVERT: A 189 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7722 (tp30) REVERT: A 227 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7778 (mm-30) REVERT: A 288 LYS cc_start: 0.8229 (ttmt) cc_final: 0.8015 (tttt) REVERT: A 297 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6787 (mtm) REVERT: A 333 LEU cc_start: 0.8923 (mp) cc_final: 0.8712 (mt) REVERT: A 423 LEU cc_start: 0.8468 (mm) cc_final: 0.8198 (mp) REVERT: A 470 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8092 (mtpp) REVERT: B 339 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7943 (t70) REVERT: B 347 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: B 357 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6107 (tmm-80) REVERT: B 509 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8046 (mtt90) outliers start: 36 outliers final: 20 residues processed: 174 average time/residue: 0.9949 time to fit residues: 182.9820 Evaluate side-chains 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 44 optimal weight: 0.5980 chunk 63 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.0010 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS A 586 ASN B 409 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129203 restraints weight = 9030.570| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.02 r_work: 0.3588 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6742 Z= 0.126 Angle : 0.644 9.802 9185 Z= 0.315 Chirality : 0.045 0.373 982 Planarity : 0.005 0.061 1173 Dihedral : 6.921 55.480 1064 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.38 % Rotamer: Outliers : 4.46 % Allowed : 20.86 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.45 (0.31), residues: 788 helix: 0.79 (0.28), residues: 371 sheet: -0.48 (0.73), residues: 41 loop : -1.41 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.001 PHE A 592 TYR 0.012 0.001 TYR B 453 ARG 0.013 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 7) link_NAG-ASN : angle 3.92771 ( 21) link_BETA1-4 : bond 0.00525 ( 1) link_BETA1-4 : angle 1.03697 ( 3) hydrogen bonds : bond 0.04072 ( 245) hydrogen bonds : angle 4.40116 ( 696) link_BETA1-6 : bond 0.00367 ( 1) link_BETA1-6 : angle 1.15981 ( 3) metal coordination : bond 0.00322 ( 2) SS BOND : bond 0.00333 ( 7) SS BOND : angle 0.85719 ( 14) covalent geometry : bond 0.00289 ( 6724) covalent geometry : angle 0.61548 ( 9144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7996 (mtpp) REVERT: A 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.7234 (tp30) REVERT: A 156 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 167 SER cc_start: 0.8459 (m) cc_final: 0.8241 (p) REVERT: A 189 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7919 (tt0) REVERT: A 227 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7717 (mm-30) REVERT: A 283 VAL cc_start: 0.8704 (p) cc_final: 0.8462 (t) REVERT: A 288 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7855 (tttt) REVERT: A 423 LEU cc_start: 0.8452 (mm) cc_final: 0.8183 (mp) REVERT: A 470 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8132 (mtpp) REVERT: B 347 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: B 357 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6123 (tmm-80) REVERT: B 509 ARG cc_start: 0.8285 (ttm170) cc_final: 0.8082 (mtt90) outliers start: 31 outliers final: 19 residues processed: 171 average time/residue: 1.0946 time to fit residues: 197.0480 Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 487 ASN B 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.146983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126692 restraints weight = 13473.601| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.55 r_work: 0.3528 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6742 Z= 0.142 Angle : 0.647 9.872 9185 Z= 0.316 Chirality : 0.045 0.365 982 Planarity : 0.005 0.060 1173 Dihedral : 6.704 55.140 1062 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.50 % Rotamer: Outliers : 4.32 % Allowed : 21.87 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.31 (0.31), residues: 788 helix: 0.91 (0.28), residues: 371 sheet: -0.30 (0.75), residues: 41 loop : -1.36 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS A 241 PHE 0.026 0.002 PHE A 603 TYR 0.014 0.002 TYR A 183 ARG 0.013 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 7) link_NAG-ASN : angle 3.88541 ( 21) link_BETA1-4 : bond 0.00411 ( 1) link_BETA1-4 : angle 1.00082 ( 3) hydrogen bonds : bond 0.04243 ( 245) hydrogen bonds : angle 4.36747 ( 696) link_BETA1-6 : bond 0.00491 ( 1) link_BETA1-6 : angle 1.16986 ( 3) metal coordination : bond 0.00622 ( 2) SS BOND : bond 0.00400 ( 7) SS BOND : angle 0.85299 ( 14) covalent geometry : bond 0.00330 ( 6724) covalent geometry : angle 0.61923 ( 9144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7283 (mp0) cc_final: 0.7033 (mp0) REVERT: A 68 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7928 (mtpp) REVERT: A 75 GLU cc_start: 0.7272 (tp30) cc_final: 0.7056 (tp30) REVERT: A 156 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 167 SER cc_start: 0.8368 (m) cc_final: 0.8149 (p) REVERT: A 177 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7315 (ttm170) REVERT: A 189 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7772 (tt0) REVERT: A 227 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7537 (mm-30) REVERT: A 423 LEU cc_start: 0.8412 (mm) cc_final: 0.8146 (mp) REVERT: A 470 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: A 474 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7284 (mpp) REVERT: B 347 PHE cc_start: 0.6013 (OUTLIER) cc_final: 0.5753 (m-80) REVERT: B 509 ARG cc_start: 0.8232 (ttm170) cc_final: 0.8005 (mtt90) outliers start: 30 outliers final: 23 residues processed: 173 average time/residue: 1.1045 time to fit residues: 201.0382 Evaluate side-chains 184 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.0170 chunk 44 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 340 GLN A 586 ASN B 409 GLN B 487 ASN B 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125929 restraints weight = 16657.770| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.91 r_work: 0.3502 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6742 Z= 0.131 Angle : 0.632 9.870 9185 Z= 0.310 Chirality : 0.045 0.375 982 Planarity : 0.005 0.065 1173 Dihedral : 6.611 55.197 1062 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 4.89 % Allowed : 22.16 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.24 (0.31), residues: 788 helix: 0.99 (0.28), residues: 370 sheet: -0.17 (0.77), residues: 41 loop : -1.36 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.006 0.001 HIS A 195 PHE 0.018 0.001 PHE A 592 TYR 0.013 0.001 TYR B 453 ARG 0.016 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 7) link_NAG-ASN : angle 3.83602 ( 21) link_BETA1-4 : bond 0.00603 ( 1) link_BETA1-4 : angle 0.99594 ( 3) hydrogen bonds : bond 0.04056 ( 245) hydrogen bonds : angle 4.30697 ( 696) link_BETA1-6 : bond 0.00590 ( 1) link_BETA1-6 : angle 1.17045 ( 3) metal coordination : bond 0.00486 ( 2) SS BOND : bond 0.00357 ( 7) SS BOND : angle 0.78804 ( 14) covalent geometry : bond 0.00302 ( 6724) covalent geometry : angle 0.60515 ( 9144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7954 (mtpp) REVERT: A 75 GLU cc_start: 0.7328 (tp30) cc_final: 0.7112 (tp30) REVERT: A 156 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 167 SER cc_start: 0.8397 (m) cc_final: 0.8187 (p) REVERT: A 177 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7295 (ttm170) REVERT: A 189 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7532 (tp30) REVERT: A 227 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: A 423 LEU cc_start: 0.8446 (mm) cc_final: 0.8176 (mp) REVERT: A 470 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8115 (mtpp) REVERT: A 474 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7375 (mpp) REVERT: B 347 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5706 (m-10) REVERT: B 509 ARG cc_start: 0.8255 (ttm170) cc_final: 0.8047 (mtt90) outliers start: 34 outliers final: 23 residues processed: 171 average time/residue: 1.0614 time to fit residues: 191.2772 Evaluate side-chains 183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 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 61 ASN A 195 HIS A 586 ASN B 409 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126516 restraints weight = 11762.136| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.31 r_work: 0.3544 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6742 Z= 0.147 Angle : 0.648 9.876 9185 Z= 0.317 Chirality : 0.045 0.365 982 Planarity : 0.005 0.061 1173 Dihedral : 6.558 55.192 1062 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 4.75 % Allowed : 22.16 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 788 helix: 1.00 (0.28), residues: 371 sheet: -0.15 (0.79), residues: 41 loop : -1.31 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS A 195 PHE 0.024 0.002 PHE A 603 TYR 0.014 0.001 TYR B 453 ARG 0.016 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 7) link_NAG-ASN : angle 3.78443 ( 21) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 0.95053 ( 3) hydrogen bonds : bond 0.04257 ( 245) hydrogen bonds : angle 4.31443 ( 696) link_BETA1-6 : bond 0.00441 ( 1) link_BETA1-6 : angle 1.13141 ( 3) metal coordination : bond 0.00673 ( 2) SS BOND : bond 0.00375 ( 7) SS BOND : angle 0.82820 ( 14) covalent geometry : bond 0.00344 ( 6724) covalent geometry : angle 0.62215 ( 9144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7916 (t80) cc_final: 0.7700 (t80) REVERT: A 68 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8082 (mtpp) REVERT: A 75 GLU cc_start: 0.7472 (tp30) cc_final: 0.7247 (tp30) REVERT: A 156 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 177 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7402 (ttm170) REVERT: A 189 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7660 (tp30) REVERT: A 227 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7782 (mm-30) REVERT: A 470 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: A 474 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7552 (mpp) REVERT: B 347 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: B 357 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6228 (tmm-80) outliers start: 33 outliers final: 21 residues processed: 168 average time/residue: 1.0804 time to fit residues: 191.6169 Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS 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 67 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127872 restraints weight = 11881.913| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.35 r_work: 0.3562 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6742 Z= 0.116 Angle : 0.619 9.867 9185 Z= 0.303 Chirality : 0.044 0.361 982 Planarity : 0.005 0.065 1173 Dihedral : 6.355 54.592 1060 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 4.17 % Allowed : 22.88 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.09 (0.31), residues: 788 helix: 1.08 (0.28), residues: 371 sheet: 0.08 (0.81), residues: 40 loop : -1.26 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.003 0.001 HIS A 374 PHE 0.023 0.001 PHE A 603 TYR 0.012 0.001 TYR B 453 ARG 0.016 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00819 ( 7) link_NAG-ASN : angle 3.73579 ( 21) link_BETA1-4 : bond 0.00523 ( 1) link_BETA1-4 : angle 0.87608 ( 3) hydrogen bonds : bond 0.03721 ( 245) hydrogen bonds : angle 4.24128 ( 696) link_BETA1-6 : bond 0.00378 ( 1) link_BETA1-6 : angle 1.18398 ( 3) metal coordination : bond 0.00306 ( 2) SS BOND : bond 0.00285 ( 7) SS BOND : angle 0.72916 ( 14) covalent geometry : bond 0.00266 ( 6724) covalent geometry : angle 0.59307 ( 9144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8077 (mtpp) REVERT: A 75 GLU cc_start: 0.7504 (tp30) cc_final: 0.7283 (tp30) REVERT: A 177 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: A 189 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7673 (tp30) REVERT: A 227 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7794 (mm-30) REVERT: B 347 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5906 (m-10) outliers start: 29 outliers final: 21 residues processed: 163 average time/residue: 1.0704 time to fit residues: 183.8760 Evaluate side-chains 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS 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 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127130 restraints weight = 11482.053| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.30 r_work: 0.3563 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6742 Z= 0.126 Angle : 0.635 9.874 9185 Z= 0.310 Chirality : 0.044 0.358 982 Planarity : 0.005 0.059 1173 Dihedral : 6.192 54.676 1058 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.63 % Rotamer: Outliers : 3.88 % Allowed : 23.17 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.31), residues: 788 helix: 1.11 (0.28), residues: 370 sheet: 0.02 (0.81), residues: 40 loop : -1.26 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.022 0.002 PHE A 603 TYR 0.013 0.001 TYR B 453 ARG 0.017 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00827 ( 7) link_NAG-ASN : angle 3.67707 ( 21) link_BETA1-4 : bond 0.00503 ( 1) link_BETA1-4 : angle 0.88115 ( 3) hydrogen bonds : bond 0.03879 ( 245) hydrogen bonds : angle 4.23297 ( 696) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.15011 ( 3) metal coordination : bond 0.00486 ( 2) SS BOND : bond 0.00314 ( 7) SS BOND : angle 0.71974 ( 14) covalent geometry : bond 0.00292 ( 6724) covalent geometry : angle 0.60995 ( 9144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.73 seconds wall clock time: 106 minutes 19.99 seconds (6379.99 seconds total)