Starting phenix.real_space_refine on Sat Aug 23 10:44:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we0_37469/08_2025/8we0_37469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we0_37469/08_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_37469/08_2025/8we0_37469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we0_37469/08_2025/8we0_37469.map" model { file = "/net/cci-nas-00/data/ceres_data/8we0_37469/08_2025/8we0_37469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we0_37469/08_2025/8we0_37469.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.32 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: 0.54 Conformation dependent library (CDL) restraints added in 443.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.16 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: 0.64 Time building geometry restraints manager: 0.68 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (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 ARG 0.003 0.000 ARG A 482 TYR 0.028 0.002 TYR B 473 PHE 0.016 0.001 PHE A 314 TRP 0.036 0.002 TRP B 353 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 6724) covalent geometry : angle 1.15323 ( 9144) SS BOND : bond 0.01269 ( 7) SS BOND : angle 1.60332 ( 14) hydrogen bonds : bond 0.21108 ( 245) hydrogen bonds : angle 7.57961 ( 696) metal coordination : bond 0.20583 ( 2) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 0.61960 ( 3) link_BETA1-6 : bond 0.00198 ( 1) link_BETA1-6 : angle 1.22596 ( 3) link_NAG-ASN : bond 0.00703 ( 7) link_NAG-ASN : angle 4.55697 ( 21) *********************** 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 : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 26 residues processed: 224 average time/residue: 0.4135 time to fit residues: 98.0104 Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 GLN A 139 GLN A 149 ASN A 340 GLN A 493 HIS B 339 HIS B 422 ASN B 439 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.150278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130184 restraints weight = 11326.906| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.37 r_work: 0.3595 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6742 Z= 0.176 Angle : 0.827 11.881 9185 Z= 0.396 Chirality : 0.055 0.710 982 Planarity : 0.008 0.117 1173 Dihedral : 9.412 59.042 1110 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.88 % Favored : 91.61 % Rotamer: Outliers : 5.61 % Allowed : 16.83 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.30), residues: 788 helix: 0.18 (0.28), residues: 386 sheet: -0.65 (0.84), residues: 41 loop : -2.11 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 582 TYR 0.015 0.002 TYR A 613 PHE 0.028 0.002 PHE A 592 TRP 0.013 0.002 TRP B 353 HIS 0.006 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6724) covalent geometry : angle 0.77898 ( 9144) SS BOND : bond 0.00457 ( 7) SS BOND : angle 1.13147 ( 14) hydrogen bonds : bond 0.05095 ( 245) hydrogen bonds : angle 5.02398 ( 696) metal coordination : bond 0.00583 ( 2) link_BETA1-4 : bond 0.00538 ( 1) link_BETA1-4 : angle 1.51363 ( 3) link_BETA1-6 : bond 0.00344 ( 1) link_BETA1-6 : angle 1.25545 ( 3) link_NAG-ASN : bond 0.00424 ( 7) link_NAG-ASN : angle 5.75879 ( 21) *********************** 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 202 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 189 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7565 (tp30) REVERT: A 227 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: A 407 ILE cc_start: 0.7557 (pt) cc_final: 0.7352 (pt) REVERT: A 468 ILE cc_start: 0.8535 (mt) cc_final: 0.8156 (tt) REVERT: A 470 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: A 564 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7929 (mm-30) outliers start: 39 outliers final: 17 residues processed: 184 average time/residue: 0.4399 time to fit residues: 85.5980 Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 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 67 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS A 330 ASN A 340 GLN A 580 ASN B 439 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126871 restraints weight = 17467.701| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.99 r_work: 0.3528 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6742 Z= 0.149 Angle : 0.711 11.368 9185 Z= 0.344 Chirality : 0.046 0.338 982 Planarity : 0.006 0.081 1173 Dihedral : 7.605 56.275 1071 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.75 % Favored : 91.99 % Rotamer: Outliers : 4.17 % Allowed : 20.14 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.30), residues: 788 helix: 0.34 (0.28), residues: 381 sheet: -0.62 (0.80), residues: 42 loop : -1.83 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 559 TYR 0.013 0.002 TYR A 613 PHE 0.018 0.002 PHE A 592 TRP 0.030 0.002 TRP B 353 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6724) covalent geometry : angle 0.68322 ( 9144) SS BOND : bond 0.00412 ( 7) SS BOND : angle 1.04231 ( 14) hydrogen bonds : bond 0.04476 ( 245) hydrogen bonds : angle 4.62882 ( 696) metal coordination : bond 0.00453 ( 2) link_BETA1-4 : bond 0.00553 ( 1) link_BETA1-4 : angle 1.39135 ( 3) link_BETA1-6 : bond 0.00449 ( 1) link_BETA1-6 : angle 1.09619 ( 3) link_NAG-ASN : bond 0.00824 ( 7) link_NAG-ASN : angle 4.07613 ( 21) *********************** 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: 29 poor density : 156 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7495 (mp0) cc_final: 0.7244 (mp0) REVERT: A 167 SER cc_start: 0.8402 (m) cc_final: 0.8193 (p) REVERT: A 189 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7438 (tp30) REVERT: A 227 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 283 VAL cc_start: 0.8600 (p) cc_final: 0.8395 (t) REVERT: A 318 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 407 ILE cc_start: 0.7420 (pt) cc_final: 0.7216 (pt) REVERT: A 470 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: A 518 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.8064 (ttp-110) REVERT: B 339 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7684 (t70) REVERT: B 347 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: B 357 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5925 (tmm-80) REVERT: B 509 ARG cc_start: 0.8229 (ttm170) cc_final: 0.8010 (mtt90) outliers start: 29 outliers final: 16 residues processed: 171 average time/residue: 0.4470 time to fit residues: 80.4224 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 195 HIS A 340 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.147885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125286 restraints weight = 21829.610| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.35 r_work: 0.3496 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6742 Z= 0.146 Angle : 0.679 9.983 9185 Z= 0.330 Chirality : 0.047 0.466 982 Planarity : 0.006 0.075 1173 Dihedral : 7.221 59.926 1066 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.50 % Rotamer: Outliers : 4.89 % Allowed : 20.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.30), residues: 788 helix: 0.61 (0.28), residues: 371 sheet: -0.57 (0.77), residues: 42 loop : -1.55 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 559 TYR 0.016 0.002 TYR A 215 PHE 0.015 0.002 PHE A 592 TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6724) covalent geometry : angle 0.64944 ( 9144) SS BOND : bond 0.00399 ( 7) SS BOND : angle 0.97996 ( 14) hydrogen bonds : bond 0.04299 ( 245) hydrogen bonds : angle 4.45880 ( 696) metal coordination : bond 0.00554 ( 2) link_BETA1-4 : bond 0.00587 ( 1) link_BETA1-4 : angle 1.19122 ( 3) link_BETA1-6 : bond 0.00418 ( 1) link_BETA1-6 : angle 1.11679 ( 3) link_NAG-ASN : bond 0.01001 ( 7) link_NAG-ASN : angle 4.08914 ( 21) *********************** 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 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7882 (t80) cc_final: 0.7676 (t80) REVERT: A 68 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8000 (mtpp) REVERT: A 189 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7512 (tp30) REVERT: A 227 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7560 (mm-30) REVERT: A 283 VAL cc_start: 0.8667 (p) cc_final: 0.8444 (t) REVERT: A 318 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8037 (p) REVERT: A 470 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8084 (mtpp) REVERT: A 474 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7319 (mpp) REVERT: B 339 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7713 (t70) REVERT: B 347 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5810 (m-80) REVERT: B 357 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6045 (tmm-80) REVERT: B 509 ARG cc_start: 0.8234 (ttm170) cc_final: 0.8023 (mtt90) outliers start: 34 outliers final: 22 residues processed: 167 average time/residue: 0.4546 time to fit residues: 80.0359 Evaluate side-chains 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN 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 334 THR 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 560 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ASP 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 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 77 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 439 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126850 restraints weight = 13027.382| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.52 r_work: 0.3541 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6742 Z= 0.144 Angle : 0.658 9.788 9185 Z= 0.321 Chirality : 0.045 0.366 982 Planarity : 0.006 0.066 1173 Dihedral : 6.886 55.750 1066 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.50 % Rotamer: Outliers : 4.32 % Allowed : 21.29 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.30), residues: 788 helix: 0.72 (0.28), residues: 371 sheet: -0.36 (0.75), residues: 41 loop : -1.49 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 559 TYR 0.013 0.001 TYR B 453 PHE 0.022 0.002 PHE A 603 TRP 0.023 0.002 TRP B 353 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6724) covalent geometry : angle 0.63133 ( 9144) SS BOND : bond 0.00387 ( 7) SS BOND : angle 0.76584 ( 14) hydrogen bonds : bond 0.04272 ( 245) hydrogen bonds : angle 4.43200 ( 696) metal coordination : bond 0.00552 ( 2) link_BETA1-4 : bond 0.00589 ( 1) link_BETA1-4 : angle 1.12459 ( 3) link_BETA1-6 : bond 0.00395 ( 1) link_BETA1-6 : angle 1.10559 ( 3) link_NAG-ASN : bond 0.00882 ( 7) link_NAG-ASN : angle 3.88696 ( 21) *********************** 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 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7899 (mtpp) REVERT: A 75 GLU cc_start: 0.7313 (tp30) cc_final: 0.7094 (tp30) REVERT: A 189 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7433 (tp30) REVERT: A 227 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7474 (mm-30) REVERT: A 283 VAL cc_start: 0.8629 (p) cc_final: 0.8392 (t) REVERT: A 423 LEU cc_start: 0.8348 (mm) cc_final: 0.8079 (mp) REVERT: A 470 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8019 (mtpp) REVERT: A 474 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7208 (mpp) REVERT: B 339 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7741 (t70) REVERT: B 347 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: B 357 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5932 (tmm-80) REVERT: B 509 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7962 (mtt90) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.4637 time to fit residues: 80.4619 Evaluate side-chains 169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR 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 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 560 LEU 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 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 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127596 restraints weight = 9188.827| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.02 r_work: 0.3581 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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 = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6742 Z= 0.157 Angle : 0.657 9.792 9185 Z= 0.323 Chirality : 0.046 0.370 982 Planarity : 0.006 0.062 1173 Dihedral : 6.742 55.773 1062 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.63 % Rotamer: Outliers : 4.32 % Allowed : 21.44 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.31), residues: 788 helix: 0.83 (0.28), residues: 371 sheet: -0.41 (0.75), residues: 41 loop : -1.42 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 559 TYR 0.015 0.002 TYR B 451 PHE 0.021 0.002 PHE A 592 TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6724) covalent geometry : angle 0.63074 ( 9144) SS BOND : bond 0.00419 ( 7) SS BOND : angle 0.81889 ( 14) hydrogen bonds : bond 0.04449 ( 245) hydrogen bonds : angle 4.45075 ( 696) metal coordination : bond 0.00591 ( 2) link_BETA1-4 : bond 0.00548 ( 1) link_BETA1-4 : angle 1.08541 ( 3) link_BETA1-6 : bond 0.00445 ( 1) link_BETA1-6 : angle 1.13419 ( 3) link_NAG-ASN : bond 0.00835 ( 7) link_NAG-ASN : angle 3.86289 ( 21) *********************** 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 184 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8025 (mtpp) REVERT: A 75 GLU cc_start: 0.7473 (tp30) cc_final: 0.7248 (tp30) REVERT: A 156 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 189 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7688 (tp30) REVERT: A 227 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 423 LEU cc_start: 0.8436 (mm) cc_final: 0.8180 (mp) REVERT: A 470 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (mtpp) REVERT: B 342 PHE cc_start: 0.8600 (m-80) cc_final: 0.8399 (m-80) REVERT: B 347 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: B 357 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6186 (tmm-80) REVERT: B 509 ARG cc_start: 0.8296 (ttm170) cc_final: 0.8080 (mtt90) outliers start: 30 outliers final: 19 residues processed: 166 average time/residue: 0.5184 time to fit residues: 90.6558 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR 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 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain 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 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 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126195 restraints weight = 17123.834| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.93 r_work: 0.3517 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6742 Z= 0.118 Angle : 0.633 9.800 9185 Z= 0.309 Chirality : 0.044 0.362 982 Planarity : 0.005 0.059 1173 Dihedral : 6.607 54.867 1062 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.39 % Rotamer: Outliers : 4.03 % Allowed : 22.88 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.31), residues: 788 helix: 0.97 (0.28), residues: 370 sheet: -0.18 (0.77), residues: 41 loop : -1.35 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 559 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE A 592 TRP 0.025 0.001 TRP B 353 HIS 0.010 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6724) covalent geometry : angle 0.60497 ( 9144) SS BOND : bond 0.00334 ( 7) SS BOND : angle 0.74434 ( 14) hydrogen bonds : bond 0.03897 ( 245) hydrogen bonds : angle 4.35436 ( 696) metal coordination : bond 0.00325 ( 2) link_BETA1-4 : bond 0.00531 ( 1) link_BETA1-4 : angle 0.96945 ( 3) link_BETA1-6 : bond 0.00463 ( 1) link_BETA1-6 : angle 1.20260 ( 3) link_NAG-ASN : bond 0.00827 ( 7) link_NAG-ASN : angle 3.86103 ( 21) *********************** 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 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7939 (mtpp) REVERT: A 156 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 189 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7523 (tp30) REVERT: A 227 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7578 (mm-30) REVERT: A 423 LEU cc_start: 0.8372 (mm) cc_final: 0.8105 (mp) REVERT: A 470 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: B 342 PHE cc_start: 0.8682 (m-80) cc_final: 0.8452 (m-80) REVERT: B 347 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: B 357 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.6114 (tmm-80) outliers start: 28 outliers final: 19 residues processed: 162 average time/residue: 0.5331 time to fit residues: 90.7147 Evaluate side-chains 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 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 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 487 ASN ** B 506 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 = 0.3944 r_free = 0.3944 target = 0.145988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126068 restraints weight = 11740.892| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.34 r_work: 0.3547 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6742 Z= 0.164 Angle : 0.654 9.842 9185 Z= 0.322 Chirality : 0.046 0.367 982 Planarity : 0.006 0.063 1173 Dihedral : 6.497 55.792 1060 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 4.32 % Allowed : 23.60 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.31), residues: 788 helix: 0.93 (0.28), residues: 372 sheet: -0.03 (0.79), residues: 41 loop : -1.32 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 559 TYR 0.018 0.002 TYR B 451 PHE 0.023 0.002 PHE A 603 TRP 0.021 0.002 TRP B 353 HIS 0.015 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6724) covalent geometry : angle 0.62794 ( 9144) SS BOND : bond 0.00425 ( 7) SS BOND : angle 0.85992 ( 14) hydrogen bonds : bond 0.04454 ( 245) hydrogen bonds : angle 4.39170 ( 696) metal coordination : bond 0.00789 ( 2) link_BETA1-4 : bond 0.00550 ( 1) link_BETA1-4 : angle 1.02221 ( 3) link_BETA1-6 : bond 0.00376 ( 1) link_BETA1-6 : angle 1.07975 ( 3) link_NAG-ASN : bond 0.00837 ( 7) link_NAG-ASN : angle 3.81953 ( 21) *********************** 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 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8055 (mtpp) REVERT: A 156 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 189 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7764 (tp30) REVERT: A 227 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7769 (mm-30) REVERT: A 423 LEU cc_start: 0.8478 (mm) cc_final: 0.8231 (mp) REVERT: A 470 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8224 (mtpp) REVERT: B 347 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5992 (m-10) outliers start: 30 outliers final: 20 residues processed: 162 average time/residue: 0.5174 time to fit residues: 88.2966 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 487 ASN ** B 506 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 = 0.3947 r_free = 0.3947 target = 0.146191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127288 restraints weight = 9208.809| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.05 r_work: 0.3579 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 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 = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6742 Z= 0.147 Angle : 0.649 9.860 9185 Z= 0.318 Chirality : 0.045 0.364 982 Planarity : 0.006 0.061 1173 Dihedral : 6.470 55.780 1060 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.38 % Rotamer: Outliers : 4.03 % Allowed : 23.74 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 788 helix: 0.98 (0.28), residues: 371 sheet: -0.06 (0.82), residues: 41 loop : -1.33 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 559 TYR 0.019 0.002 TYR B 451 PHE 0.018 0.002 PHE A 592 TRP 0.022 0.002 TRP B 353 HIS 0.017 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6724) covalent geometry : angle 0.62326 ( 9144) SS BOND : bond 0.00383 ( 7) SS BOND : angle 0.82521 ( 14) hydrogen bonds : bond 0.04293 ( 245) hydrogen bonds : angle 4.36898 ( 696) metal coordination : bond 0.00645 ( 2) link_BETA1-4 : bond 0.00596 ( 1) link_BETA1-4 : angle 0.99349 ( 3) link_BETA1-6 : bond 0.00392 ( 1) link_BETA1-6 : angle 1.12274 ( 3) link_NAG-ASN : bond 0.00817 ( 7) link_NAG-ASN : angle 3.79369 ( 21) *********************** 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 176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8022 (mtpp) REVERT: A 156 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 189 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7697 (tp30) REVERT: A 227 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7711 (mm-30) REVERT: A 423 LEU cc_start: 0.8484 (mm) cc_final: 0.8227 (mp) REVERT: A 470 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (mtpp) REVERT: B 347 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.6006 (m-10) REVERT: B 357 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6143 (tmm-80) outliers start: 28 outliers final: 21 residues processed: 159 average time/residue: 0.4799 time to fit residues: 80.3464 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 : 0.195 ------------------------------------------------------------------------------- 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 86 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 TRP 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 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 487 ASN ** B 506 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 = 0.3930 r_free = 0.3930 target = 0.145032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123526 restraints weight = 17620.813| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.94 r_work: 0.3478 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6742 Z= 0.166 Angle : 0.662 9.849 9185 Z= 0.326 Chirality : 0.046 0.359 982 Planarity : 0.006 0.061 1173 Dihedral : 6.479 56.038 1060 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % Rotamer: Outliers : 4.17 % Allowed : 23.45 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.31), residues: 788 helix: 1.07 (0.28), residues: 365 sheet: -0.31 (0.80), residues: 41 loop : -1.35 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 559 TYR 0.024 0.002 TYR B 451 PHE 0.019 0.002 PHE A 592 TRP 0.020 0.002 TRP B 353 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6724) covalent geometry : angle 0.63727 ( 9144) SS BOND : bond 0.00429 ( 7) SS BOND : angle 0.88552 ( 14) hydrogen bonds : bond 0.04531 ( 245) hydrogen bonds : angle 4.42141 ( 696) metal coordination : bond 0.00840 ( 2) link_BETA1-4 : bond 0.00572 ( 1) link_BETA1-4 : angle 0.98574 ( 3) link_BETA1-6 : bond 0.00413 ( 1) link_BETA1-6 : angle 1.09696 ( 3) link_NAG-ASN : bond 0.00815 ( 7) link_NAG-ASN : angle 3.74912 ( 21) ********************** 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 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8005 (mtpp) REVERT: A 156 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 189 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7632 (tp30) REVERT: A 423 LEU cc_start: 0.8443 (mm) cc_final: 0.8200 (mp) REVERT: A 470 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: B 347 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: B 357 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6124 (tmm-80) outliers start: 29 outliers final: 21 residues processed: 159 average time/residue: 0.5018 time to fit residues: 84.1793 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 : 0.250 ------------------------------------------------------------------------------- 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 86 GLN Chi-restraints excluded: chain A residue 92 THR 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 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 578 ASN 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 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 409 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127601 restraints weight = 9611.886| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.05 r_work: 0.3592 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 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 = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6742 Z= 0.126 Angle : 0.636 9.842 9185 Z= 0.312 Chirality : 0.044 0.354 982 Planarity : 0.005 0.059 1173 Dihedral : 6.229 55.131 1058 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 3.74 % Allowed : 24.03 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.31), residues: 788 helix: 1.18 (0.28), residues: 364 sheet: -0.43 (0.80), residues: 41 loop : -1.32 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 559 TYR 0.015 0.001 TYR B 451 PHE 0.015 0.001 PHE A 592 TRP 0.024 0.001 TRP B 353 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6724) covalent geometry : angle 0.61118 ( 9144) SS BOND : bond 0.00316 ( 7) SS BOND : angle 0.74384 ( 14) hydrogen bonds : bond 0.04011 ( 245) hydrogen bonds : angle 4.33591 ( 696) metal coordination : bond 0.00397 ( 2) link_BETA1-4 : bond 0.00536 ( 1) link_BETA1-4 : angle 0.89030 ( 3) link_BETA1-6 : bond 0.00332 ( 1) link_BETA1-6 : angle 1.16558 ( 3) link_NAG-ASN : bond 0.00795 ( 7) link_NAG-ASN : angle 3.70371 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2729.35 seconds wall clock time: 46 minutes 58.72 seconds (2818.72 seconds total)