Starting phenix.real_space_refine on Tue Jun 10 10:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we0_37469/06_2025/8we0_37469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we0_37469/06_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_37469/06_2025/8we0_37469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we0_37469/06_2025/8we0_37469.map" model { file = "/net/cci-nas-00/data/ceres_data/8we0_37469/06_2025/8we0_37469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we0_37469/06_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-5710/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: 6.55, per 1000 atoms: 1.00 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: 1.94 Conformation dependent library (CDL) restraints added in 1.4 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: 0.67 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: 1.63 Time building geometry restraints manager: 2.25 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- 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 : 0.640 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: 1.0693 time to fit residues: 252.5484 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 : 0.634 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130666 restraints weight = 16616.951| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.00 r_work: 0.3579 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 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 = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 11.581 9185 Z= 0.382 Chirality : 0.052 0.610 982 Planarity : 0.007 0.107 1173 Dihedral : 9.468 58.029 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 5.63190 ( 21) link_BETA1-4 : bond 0.00794 ( 1) link_BETA1-4 : angle 1.47930 ( 3) hydrogen bonds : bond 0.04647 ( 245) hydrogen bonds : angle 4.95234 ( 696) link_BETA1-6 : bond 0.00325 ( 1) link_BETA1-6 : angle 1.44217 ( 3) metal coordination : bond 0.00200 ( 2) SS BOND : bond 0.00382 ( 7) SS BOND : angle 1.12671 ( 14) covalent geometry : bond 0.00324 ( 6724) covalent geometry : angle 0.75349 ( 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 : 0.665 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7345 (tp30) REVERT: A 227 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 407 ILE cc_start: 0.7516 (pt) cc_final: 0.7303 (pt) REVERT: A 468 ILE cc_start: 0.8451 (mt) cc_final: 0.8081 (tt) REVERT: A 470 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: B 357 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5926 (tmm-80) outliers start: 37 outliers final: 17 residues processed: 182 average time/residue: 1.0535 time to fit residues: 202.5186 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 : 0.728 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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** ** B 493 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.150002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127285 restraints weight = 21696.593| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.39 r_work: 0.3502 rms_B_bonded: 3.76 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 = 0.42 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6742 Z= 0.142 Angle : 0.700 11.821 9185 Z= 0.339 Chirality : 0.045 0.330 982 Planarity : 0.006 0.082 1173 Dihedral : 7.707 55.535 1075 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.01 % Favored : 91.74 % Rotamer: Outliers : 4.32 % Allowed : 19.14 % Favored : 76.55 % 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: -0.85 (0.30), residues: 788 helix: 0.47 (0.28), residues: 375 sheet: -0.60 (0.80), residues: 42 loop : -1.67 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.004 0.001 HIS A 505 PHE 0.021 0.002 PHE A 592 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 0.00861 ( 7) link_NAG-ASN : angle 3.89977 ( 21) link_BETA1-4 : bond 0.00460 ( 1) link_BETA1-4 : angle 1.43034 ( 3) hydrogen bonds : bond 0.04484 ( 245) hydrogen bonds : angle 4.55338 ( 696) link_BETA1-6 : bond 0.00569 ( 1) link_BETA1-6 : angle 1.07807 ( 3) metal coordination : bond 0.00491 ( 2) SS BOND : bond 0.00325 ( 7) SS BOND : angle 0.96816 ( 14) covalent geometry : bond 0.00321 ( 6724) covalent geometry : angle 0.67484 ( 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 185 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 189 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7459 (tp30) REVERT: A 227 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: A 283 VAL cc_start: 0.8594 (p) cc_final: 0.8393 (t) REVERT: A 288 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7952 (tttt) REVERT: A 470 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: A 499 ASP cc_start: 0.7872 (m-30) cc_final: 0.7604 (m-30) REVERT: B 339 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7621 (t70) REVERT: B 347 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: B 509 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8005 (mtt90) outliers start: 30 outliers final: 18 residues processed: 170 average time/residue: 0.9876 time to fit residues: 178.0481 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain A residue 223 ILE 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 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: 2.9990 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 72 optimal weight: 0.0980 chunk 56 optimal weight: 0.0970 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.152114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132452 restraints weight = 11322.802| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.33 r_work: 0.3621 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6742 Z= 0.111 Angle : 0.639 9.887 9185 Z= 0.310 Chirality : 0.044 0.386 982 Planarity : 0.005 0.076 1173 Dihedral : 7.315 56.110 1070 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.99 % Favored : 92.76 % Rotamer: Outliers : 5.04 % Allowed : 20.00 % Favored : 74.96 % 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: -0.47 (0.31), residues: 788 helix: 0.76 (0.28), residues: 369 sheet: -0.53 (0.79), residues: 42 loop : -1.38 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.003 0.001 HIS A 265 PHE 0.011 0.001 PHE A 592 TYR 0.012 0.001 TYR A 516 ARG 0.013 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00956 ( 7) link_NAG-ASN : angle 3.94109 ( 21) link_BETA1-4 : bond 0.00610 ( 1) link_BETA1-4 : angle 1.10727 ( 3) hydrogen bonds : bond 0.03587 ( 245) hydrogen bonds : angle 4.31975 ( 696) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 1.23857 ( 3) metal coordination : bond 0.00197 ( 2) SS BOND : bond 0.00380 ( 7) SS BOND : angle 0.91791 ( 14) covalent geometry : bond 0.00244 ( 6724) covalent geometry : angle 0.60977 ( 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 183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7929 (mtpp) REVERT: A 189 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7546 (tp30) REVERT: A 227 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: A 470 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (mtpp) REVERT: B 347 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: B 357 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6073 (tmm-80) REVERT: B 500 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7584 (p) outliers start: 35 outliers final: 20 residues processed: 164 average time/residue: 1.4249 time to fit residues: 246.7515 Evaluate side-chains 174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 112 LYS 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 332 MET 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 578 ASN Chi-restraints excluded: chain A residue 609 ASP 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 64 optimal weight: 0.0050 chunk 60 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 508 ASN B 409 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.147935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128363 restraints weight = 10805.310| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.23 r_work: 0.3576 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2938 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= 0.151 Angle : 0.658 9.700 9185 Z= 0.320 Chirality : 0.045 0.370 982 Planarity : 0.005 0.065 1173 Dihedral : 7.010 55.244 1068 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 5.32 % Allowed : 20.86 % 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: -0.50 (0.30), residues: 788 helix: 0.73 (0.28), residues: 377 sheet: -0.23 (0.78), residues: 41 loop : -1.49 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.022 0.002 PHE A 603 TYR 0.013 0.002 TYR A 385 ARG 0.012 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00829 ( 7) link_NAG-ASN : angle 3.85292 ( 21) link_BETA1-4 : bond 0.00400 ( 1) link_BETA1-4 : angle 1.11156 ( 3) hydrogen bonds : bond 0.04307 ( 245) hydrogen bonds : angle 4.34441 ( 696) link_BETA1-6 : bond 0.00375 ( 1) link_BETA1-6 : angle 1.07197 ( 3) metal coordination : bond 0.00704 ( 2) SS BOND : bond 0.00376 ( 7) SS BOND : angle 0.82021 ( 14) covalent geometry : bond 0.00354 ( 6724) covalent geometry : angle 0.63159 ( 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 195 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7966 (mtpp) REVERT: A 189 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7611 (tp30) REVERT: A 227 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7693 (mm-30) REVERT: A 423 LEU cc_start: 0.8445 (mm) cc_final: 0.8184 (mp) REVERT: A 470 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: B 339 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7794 (t70) REVERT: B 347 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5858 (m-80) outliers start: 37 outliers final: 20 residues processed: 175 average time/residue: 1.7083 time to fit residues: 316.2084 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 262 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS 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 578 ASN Chi-restraints excluded: chain B residue 338 PHE 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 437 ASN 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: 0.9980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129995 restraints weight = 9087.982| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.08 r_work: 0.3586 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6742 Z= 0.157 Angle : 0.661 9.811 9185 Z= 0.324 Chirality : 0.046 0.363 982 Planarity : 0.005 0.060 1173 Dihedral : 6.834 55.673 1064 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 4.89 % Allowed : 21.01 % Favored : 74.10 % 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: -0.49 (0.30), residues: 788 helix: 0.74 (0.28), residues: 377 sheet: -0.30 (0.78), residues: 41 loop : -1.47 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.005 0.001 HIS A 241 PHE 0.025 0.002 PHE A 592 TYR 0.017 0.002 TYR A 215 ARG 0.013 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 7) link_NAG-ASN : angle 3.81154 ( 21) link_BETA1-4 : bond 0.00513 ( 1) link_BETA1-4 : angle 1.10155 ( 3) hydrogen bonds : bond 0.04375 ( 245) hydrogen bonds : angle 4.36023 ( 696) link_BETA1-6 : bond 0.00387 ( 1) link_BETA1-6 : angle 1.08578 ( 3) metal coordination : bond 0.00680 ( 2) SS BOND : bond 0.00403 ( 7) SS BOND : angle 0.84426 ( 14) covalent geometry : bond 0.00368 ( 6724) covalent geometry : angle 0.63522 ( 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 188 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7996 (mtpp) REVERT: A 112 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7908 (mtpt) REVERT: A 156 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 167 SER cc_start: 0.8474 (m) cc_final: 0.8243 (p) REVERT: A 177 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: A 189 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7632 (tp30) REVERT: A 227 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7729 (mm-30) REVERT: A 423 LEU cc_start: 0.8459 (mm) cc_final: 0.8204 (mp) REVERT: A 470 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: A 474 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: B 339 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7873 (t70) REVERT: B 347 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.5942 (m-80) REVERT: B 357 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6057 (tmm-80) outliers start: 34 outliers final: 19 residues processed: 168 average time/residue: 1.4334 time to fit residues: 254.8566 Evaluate side-chains 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS 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 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 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: 3.9990 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126763 restraints weight = 13646.970| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.54 r_work: 0.3544 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6742 Z= 0.137 Angle : 0.643 9.820 9185 Z= 0.315 Chirality : 0.045 0.350 982 Planarity : 0.005 0.058 1173 Dihedral : 6.670 55.121 1062 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.99 % Favored : 92.76 % Rotamer: Outliers : 4.75 % Allowed : 21.87 % Favored : 73.38 % 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: -0.36 (0.31), residues: 788 helix: 0.82 (0.28), residues: 378 sheet: -0.08 (0.79), residues: 41 loop : -1.41 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.010 0.001 HIS A 195 PHE 0.023 0.002 PHE A 603 TYR 0.018 0.001 TYR A 183 ARG 0.016 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 7) link_NAG-ASN : angle 3.77125 ( 21) link_BETA1-4 : bond 0.00520 ( 1) link_BETA1-4 : angle 0.98064 ( 3) hydrogen bonds : bond 0.04152 ( 245) hydrogen bonds : angle 4.34765 ( 696) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.03303 ( 3) metal coordination : bond 0.00542 ( 2) SS BOND : bond 0.00373 ( 7) SS BOND : angle 0.82832 ( 14) covalent geometry : bond 0.00317 ( 6724) covalent geometry : angle 0.61700 ( 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 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7896 (mtpp) REVERT: A 156 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 167 SER cc_start: 0.8370 (m) cc_final: 0.8163 (p) REVERT: A 189 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7491 (tp30) REVERT: A 227 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7509 (mm-30) REVERT: A 318 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7939 (p) REVERT: A 423 LEU cc_start: 0.8355 (mm) cc_final: 0.8099 (mp) REVERT: A 470 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (mtpp) REVERT: A 474 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7356 (mpp) REVERT: B 347 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: B 357 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.6103 (tmm-80) outliers start: 33 outliers final: 18 residues processed: 168 average time/residue: 1.0467 time to fit residues: 185.4742 Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 195 HIS 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 474 MET Chi-restraints excluded: chain A residue 487 VAL 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 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: 0.7980 chunk 63 optimal weight: 0.0070 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 33 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.148676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127043 restraints weight = 16695.904| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.91 r_work: 0.3536 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3343 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= 0.113 Angle : 0.619 9.809 9185 Z= 0.303 Chirality : 0.044 0.359 982 Planarity : 0.005 0.057 1173 Dihedral : 6.525 54.421 1062 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.99 % Favored : 92.76 % Rotamer: Outliers : 4.75 % Allowed : 21.73 % Favored : 73.53 % 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: 1.04 (0.28), residues: 371 sheet: 0.05 (0.82), residues: 41 loop : -1.39 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.015 0.001 HIS A 195 PHE 0.015 0.001 PHE A 592 TYR 0.012 0.001 TYR B 453 ARG 0.012 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 7) link_NAG-ASN : angle 3.77506 ( 21) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 0.93808 ( 3) hydrogen bonds : bond 0.03733 ( 245) hydrogen bonds : angle 4.26853 ( 696) link_BETA1-6 : bond 0.00788 ( 1) link_BETA1-6 : angle 1.10825 ( 3) metal coordination : bond 0.00271 ( 2) SS BOND : bond 0.00296 ( 7) SS BOND : angle 0.74511 ( 14) covalent geometry : bond 0.00255 ( 6724) covalent geometry : angle 0.59173 ( 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 183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7921 (mtpp) REVERT: A 156 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8502 (mp) REVERT: A 167 SER cc_start: 0.8399 (m) cc_final: 0.8158 (p) REVERT: A 189 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7540 (tp30) REVERT: A 227 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 423 LEU cc_start: 0.8407 (mm) cc_final: 0.8138 (mp) REVERT: B 347 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: B 357 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6062 (tmm-80) outliers start: 33 outliers final: 19 residues processed: 163 average time/residue: 1.0396 time to fit residues: 178.7662 Evaluate side-chains 168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 445 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 487 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124157 restraints weight = 11802.719| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.33 r_work: 0.3532 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6742 Z= 0.215 Angle : 0.691 9.894 9185 Z= 0.342 Chirality : 0.048 0.359 982 Planarity : 0.006 0.061 1173 Dihedral : 6.730 56.610 1062 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.26 % Favored : 91.49 % Rotamer: Outliers : 4.75 % Allowed : 22.30 % 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: -0.39 (0.31), residues: 788 helix: 0.84 (0.28), residues: 371 sheet: -0.01 (0.83), residues: 41 loop : -1.45 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 163 HIS 0.007 0.002 HIS A 195 PHE 0.023 0.002 PHE A 512 TYR 0.024 0.002 TYR B 451 ARG 0.015 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00850 ( 7) link_NAG-ASN : angle 3.79529 ( 21) link_BETA1-4 : bond 0.00405 ( 1) link_BETA1-4 : angle 1.06411 ( 3) hydrogen bonds : bond 0.05016 ( 245) hydrogen bonds : angle 4.44166 ( 696) link_BETA1-6 : bond 0.00486 ( 1) link_BETA1-6 : angle 1.03084 ( 3) metal coordination : bond 0.01177 ( 2) SS BOND : bond 0.00527 ( 7) SS BOND : angle 0.98774 ( 14) covalent geometry : bond 0.00507 ( 6724) covalent geometry : angle 0.66704 ( 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 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8112 (mtpp) REVERT: A 177 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7488 (ttm170) REVERT: A 189 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7766 (tp30) REVERT: A 227 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7823 (mm-30) REVERT: A 423 LEU cc_start: 0.8504 (mm) cc_final: 0.8248 (mp) REVERT: B 347 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.6016 (m-80) outliers start: 33 outliers final: 22 residues processed: 163 average time/residue: 1.0397 time to fit residues: 179.3210 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 VAL 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 471 ASP Chi-restraints excluded: chain A residue 487 VAL 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: 0.9980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 chunk 26 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.148276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128715 restraints weight = 11892.330| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.34 r_work: 0.3585 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3629 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= 0.111 Angle : 0.622 9.773 9185 Z= 0.305 Chirality : 0.043 0.352 982 Planarity : 0.005 0.057 1173 Dihedral : 6.461 54.376 1062 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 3.60 % Allowed : 23.74 % Favored : 72.66 % 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: 1.03 (0.28), residues: 370 sheet: 0.23 (0.86), residues: 40 loop : -1.39 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.003 0.001 HIS A 265 PHE 0.024 0.001 PHE A 603 TYR 0.012 0.001 TYR A 215 ARG 0.014 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 7) link_NAG-ASN : angle 3.71911 ( 21) link_BETA1-4 : bond 0.00548 ( 1) link_BETA1-4 : angle 0.87221 ( 3) hydrogen bonds : bond 0.03612 ( 245) hydrogen bonds : angle 4.22769 ( 696) link_BETA1-6 : bond 0.00261 ( 1) link_BETA1-6 : angle 1.22902 ( 3) metal coordination : bond 0.00115 ( 2) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.71187 ( 14) covalent geometry : bond 0.00249 ( 6724) covalent geometry : angle 0.59601 ( 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 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8061 (mtpp) REVERT: A 189 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7674 (tp30) REVERT: A 227 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: A 323 MET cc_start: 0.7031 (mmm) cc_final: 0.6125 (mmm) REVERT: A 423 LEU cc_start: 0.8515 (mm) cc_final: 0.8260 (mp) REVERT: B 347 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5957 (m-80) REVERT: B 357 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6180 (tmm-80) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 1.0940 time to fit residues: 181.1397 Evaluate side-chains 165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 578 ASN 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: 1.9990 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127713 restraints weight = 11436.576| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.29 r_work: 0.3583 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3602 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= 0.122 Angle : 0.625 9.831 9185 Z= 0.306 Chirality : 0.044 0.349 982 Planarity : 0.005 0.058 1173 Dihedral : 6.193 54.501 1058 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.50 % Rotamer: Outliers : 3.31 % Allowed : 24.17 % Favored : 72.52 % 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: -0.13 (0.31), residues: 788 helix: 1.09 (0.28), residues: 370 sheet: 0.25 (0.85), residues: 40 loop : -1.36 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.003 0.001 HIS A 374 PHE 0.026 0.002 PHE A 603 TYR 0.013 0.001 TYR B 453 ARG 0.015 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 7) link_NAG-ASN : angle 3.63391 ( 21) link_BETA1-4 : bond 0.00502 ( 1) link_BETA1-4 : angle 0.90700 ( 3) hydrogen bonds : bond 0.03806 ( 245) hydrogen bonds : angle 4.18812 ( 696) link_BETA1-6 : bond 0.00394 ( 1) link_BETA1-6 : angle 1.16047 ( 3) metal coordination : bond 0.00433 ( 2) SS BOND : bond 0.00308 ( 7) SS BOND : angle 0.72767 ( 14) covalent geometry : bond 0.00283 ( 6724) covalent geometry : angle 0.60078 ( 9144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6940.10 seconds wall clock time: 122 minutes 48.94 seconds (7368.94 seconds total)