Starting phenix.real_space_refine on Sun Aug 4 21:53:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_37469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_37469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_37469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_37469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we0_37469/08_2024/8we0_37469.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6315 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4182 2.51 5 N 1074 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6538 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.27, per 1000 atoms: 0.96 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 - 3.50 Amino acid : False - 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: 2.72 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 906 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 49.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.844A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.852A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.680A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.951A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.593A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.606A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.639A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 4.396A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.591A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.663A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.556A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.734A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.560A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.710A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.817A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.555A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.277A pdb=" N ILE B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.491A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.515A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.190A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.672A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 245 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 2.97 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: 99.86 - 106.76: 266 106.76 - 113.66: 3510 113.66 - 120.55: 2932 120.55 - 127.45: 2354 127.45 - 134.34: 82 Bond angle restraints: 9144 Sorted by residual: angle pdb=" N GLU B 340 " pdb=" CA GLU B 340 " pdb=" C GLU B 340 " ideal model delta sigma weight residual 113.88 104.08 9.80 1.23e+00 6.61e-01 6.35e+01 angle pdb=" N PRO A 321 " pdb=" CA PRO A 321 " pdb=" C PRO A 321 " ideal model delta sigma weight residual 110.40 122.23 -11.83 1.61e+00 3.86e-01 5.39e+01 angle pdb=" N LYS A 475 " pdb=" CA LYS A 475 " pdb=" C LYS A 475 " ideal model delta sigma weight residual 113.12 104.52 8.60 1.25e+00 6.40e-01 4.73e+01 angle pdb=" C ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta sigma weight residual 111.83 101.38 10.45 1.60e+00 3.91e-01 4.26e+01 angle pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" O GLY A 605 " ideal model delta sigma weight residual 122.37 117.67 4.70 7.30e-01 1.88e+00 4.15e+01 ... (remaining 9139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 3781 26.41 - 52.83: 252 52.83 - 79.24: 42 79.24 - 105.65: 9 105.65 - 132.06: 1 Dihedral angle restraints: 4085 sinusoidal: 1757 harmonic: 2328 Sorted by residual: dihedral pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " pdb=" CZ ARG B 355 " pdb=" NH1 ARG B 355 " ideal model delta sinusoidal sigma weight residual 0.00 -77.86 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " pdb=" NH1 ARG B 357 " ideal model delta sinusoidal sigma weight residual 0.00 -73.16 73.16 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CD ARG A 582 " pdb=" NE ARG A 582 " pdb=" CZ ARG A 582 " pdb=" NH1 ARG A 582 " ideal model delta sinusoidal sigma weight residual 0.00 -48.23 48.23 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 4082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.911: 979 0.911 - 1.821: 0 1.821 - 2.732: 0 2.732 - 3.643: 0 3.643 - 4.554: 3 Chirality restraints: 982 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 2.15 -4.55 2.00e-01 2.50e+01 5.18e+02 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 1.61 -4.01 2.00e-01 2.50e+01 4.02e+02 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 1.36 -3.76 2.00e-01 2.50e+01 3.54e+02 ... (remaining 979 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.311 2.00e-02 2.50e+03 2.70e-01 9.09e+02 pdb=" C7 NAG B 601 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 905 " -0.311 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG A 905 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 905 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 905 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG A 905 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.307 2.00e-02 2.50e+03 2.62e-01 8.57e+02 pdb=" C7 NAG A 902 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.458 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " 0.053 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 5502 3.16 - 3.74: 10134 3.74 - 4.32: 13916 4.32 - 4.90: 22576 Nonbonded interactions: 52195 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 906 " model vdw 2.000 2.230 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.220 3.120 nonbonded pdb=" O ASP A 597 " pdb=" NZ LYS A 600 " model vdw 2.222 3.120 nonbonded pdb=" NH1 ARG A 192 " pdb=" O GLU A 197 " model vdw 2.274 3.120 ... (remaining 52190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 : 0.007 0.059 6724 Z= 0.437 Angle : 1.153 11.825 9144 Z= 0.759 Chirality : 0.238 4.554 982 Planarity : 0.029 0.480 1173 Dihedral : 17.154 132.065 2570 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 3.30 % Allowed : 10.04 % Favored : 86.66 % Rotamer: Outliers : 8.20 % Allowed : 6.76 % Favored : 85.04 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.31), residues: 788 helix: -0.06 (0.29), residues: 355 sheet: -0.31 (0.90), residues: 37 loop : -2.22 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 353 HIS 0.006 0.001 HIS A 378 PHE 0.016 0.001 PHE A 314 TYR 0.028 0.002 TYR B 473 ARG 0.003 0.000 ARG A 482 *********************** 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 fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 189 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7072 (tp30) REVERT: A 291 ILE cc_start: 0.8427 (mt) cc_final: 0.8207 (mp) REVERT: A 324 THR cc_start: 0.7713 (p) cc_final: 0.7484 (p) REVERT: A 331 SER cc_start: 0.8187 (t) cc_final: 0.7833 (p) REVERT: B 383 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 513 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7318 (mt) outliers start: 57 outliers final: 27 residues processed: 224 average time/residue: 1.0136 time to fit residues: 239.9960 Evaluate side-chains 194 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.0570 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 GLN A 139 GLN A 149 ASN A 330 ASN A 340 GLN A 493 HIS B 339 HIS B 422 ASN B 439 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6724 Z= 0.189 Angle : 0.743 9.175 9144 Z= 0.367 Chirality : 0.051 0.608 982 Planarity : 0.007 0.111 1173 Dihedral : 9.448 58.906 1114 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.26 % Favored : 91.23 % Rotamer: Outliers : 5.32 % Allowed : 17.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.30), residues: 788 helix: 0.25 (0.28), residues: 383 sheet: -0.55 (0.88), residues: 41 loop : -2.05 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A 195 PHE 0.025 0.002 PHE A 592 TYR 0.013 0.001 TYR B 423 ARG 0.012 0.001 ARG A 582 *********************** 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 193 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6919 (tp30) REVERT: A 227 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: A 313 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6928 (ptpt) REVERT: A 407 ILE cc_start: 0.7412 (pt) cc_final: 0.7201 (pt) REVERT: A 468 ILE cc_start: 0.8325 (mt) cc_final: 0.7961 (tt) REVERT: A 470 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7797 (mtpp) REVERT: A 564 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7233 (mm-30) outliers start: 37 outliers final: 18 residues processed: 180 average time/residue: 1.0180 time to fit residues: 193.6138 Evaluate side-chains 176 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS 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 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 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 149 ASN A 195 HIS A 580 ASN B 437 ASN B 439 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6724 Z= 0.238 Angle : 0.694 11.065 9144 Z= 0.346 Chirality : 0.046 0.344 982 Planarity : 0.006 0.080 1173 Dihedral : 7.858 56.458 1079 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.01 % Favored : 91.74 % Rotamer: Outliers : 4.03 % Allowed : 19.71 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.30), residues: 788 helix: 0.40 (0.28), residues: 378 sheet: -0.53 (0.79), residues: 42 loop : -1.74 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 353 HIS 0.006 0.001 HIS A 505 PHE 0.023 0.002 PHE A 592 TYR 0.015 0.002 TYR A 183 ARG 0.011 0.001 ARG A 559 *********************** 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 fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 189 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6991 (tp30) REVERT: A 227 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 283 VAL cc_start: 0.8507 (p) cc_final: 0.8298 (t) REVERT: A 407 ILE cc_start: 0.7339 (pt) cc_final: 0.7134 (pt) REVERT: A 470 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7870 (mtpp) REVERT: A 499 ASP cc_start: 0.7698 (m-30) cc_final: 0.7418 (m-30) REVERT: B 339 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7485 (t70) REVERT: B 509 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7740 (mtt90) outliers start: 28 outliers final: 18 residues processed: 173 average time/residue: 1.0594 time to fit residues: 193.2371 Evaluate side-chains 172 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain B residue 339 HIS 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 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: 0.6980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 340 GLN B 437 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6724 Z= 0.215 Angle : 0.654 9.765 9144 Z= 0.325 Chirality : 0.046 0.396 982 Planarity : 0.006 0.074 1173 Dihedral : 7.635 59.858 1074 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.88 % Favored : 91.87 % Rotamer: Outliers : 4.89 % Allowed : 20.29 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.30), residues: 788 helix: 0.54 (0.28), residues: 377 sheet: -0.64 (0.78), residues: 42 loop : -1.54 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.002 PHE A 592 TYR 0.013 0.002 TYR A 183 ARG 0.012 0.001 ARG A 559 *********************** 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 184 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7762 (mtpp) REVERT: A 177 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6979 (ttm170) REVERT: A 189 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7028 (tp30) REVERT: A 227 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7053 (mm-30) REVERT: A 283 VAL cc_start: 0.8500 (p) cc_final: 0.8285 (t) REVERT: A 318 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7783 (p) REVERT: A 470 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7951 (mtpp) REVERT: A 474 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6721 (mpp) REVERT: B 339 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7448 (t70) REVERT: B 509 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7814 (mtt90) outliers start: 34 outliers final: 23 residues processed: 168 average time/residue: 1.0625 time to fit residues: 188.3635 Evaluate side-chains 173 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS B 409 GLN B 437 ASN B 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6724 Z= 0.352 Angle : 0.723 9.900 9144 Z= 0.364 Chirality : 0.050 0.375 982 Planarity : 0.006 0.066 1173 Dihedral : 7.398 58.555 1072 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.01 % Favored : 91.74 % Rotamer: Outliers : 5.61 % Allowed : 19.57 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.30), residues: 788 helix: 0.44 (0.27), residues: 377 sheet: -0.64 (0.72), residues: 42 loop : -1.60 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.007 0.002 HIS A 505 PHE 0.027 0.002 PHE A 512 TYR 0.021 0.002 TYR B 451 ARG 0.014 0.001 ARG A 559 *********************** 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 198 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7797 (mtpp) REVERT: A 156 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 167 SER cc_start: 0.8088 (m) cc_final: 0.7846 (p) REVERT: A 177 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7000 (ttm170) REVERT: A 189 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7443 (tt0) REVERT: A 227 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7165 (mm-30) REVERT: A 423 LEU cc_start: 0.8277 (mm) cc_final: 0.8005 (mp) REVERT: A 455 MET cc_start: 0.7444 (tmm) cc_final: 0.7136 (tmm) REVERT: A 470 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (mtpp) REVERT: A 474 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.6649 (mpp) REVERT: B 339 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7667 (t70) REVERT: B 509 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7740 (mtt90) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 1.0479 time to fit residues: 194.5658 Evaluate side-chains 176 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 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 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.0010 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 149 ASN A 195 HIS B 409 GLN B 437 ASN B 439 ASN B 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6724 Z= 0.192 Angle : 0.636 9.835 9144 Z= 0.320 Chirality : 0.045 0.365 982 Planarity : 0.006 0.060 1173 Dihedral : 6.981 57.112 1064 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 4.17 % Allowed : 22.01 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 788 helix: 0.66 (0.28), residues: 377 sheet: -0.66 (0.73), residues: 42 loop : -1.55 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.013 0.001 HIS A 195 PHE 0.021 0.001 PHE A 592 TYR 0.013 0.001 TYR B 423 ARG 0.013 0.001 ARG A 559 *********************** 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 fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7723 (p) REVERT: A 68 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7777 (mtpp) REVERT: A 156 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 167 SER cc_start: 0.8124 (m) cc_final: 0.7872 (p) REVERT: A 177 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7397 (tpp80) REVERT: A 189 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7238 (tp30) REVERT: A 227 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7136 (mm-30) REVERT: A 423 LEU cc_start: 0.8270 (mm) cc_final: 0.7996 (mp) REVERT: A 470 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7856 (mtpp) REVERT: B 509 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7799 (mtt90) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 1.2001 time to fit residues: 213.1862 Evaluate side-chains 174 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 223 ILE 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 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6724 Z= 0.255 Angle : 0.650 9.890 9144 Z= 0.328 Chirality : 0.046 0.374 982 Planarity : 0.006 0.062 1173 Dihedral : 6.952 56.910 1064 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.88 % Favored : 91.87 % Rotamer: Outliers : 4.32 % Allowed : 21.58 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 788 helix: 0.69 (0.28), residues: 377 sheet: -0.56 (0.72), residues: 42 loop : -1.52 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.019 0.002 HIS A 195 PHE 0.023 0.002 PHE A 603 TYR 0.019 0.002 TYR B 453 ARG 0.013 0.001 ARG A 559 *********************** 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 180 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 23 GLU cc_start: 0.6921 (mp0) cc_final: 0.6679 (mp0) REVERT: A 68 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7781 (mtpp) REVERT: A 156 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 167 SER cc_start: 0.8128 (m) cc_final: 0.7893 (p) REVERT: A 177 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: A 189 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7262 (tp30) REVERT: A 227 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7182 (mm-30) REVERT: A 318 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7796 (p) REVERT: A 423 LEU cc_start: 0.8304 (mm) cc_final: 0.8040 (mp) REVERT: A 470 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7847 (mtpp) REVERT: A 474 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6676 (mpp) REVERT: B 509 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7803 (mtt90) outliers start: 30 outliers final: 20 residues processed: 163 average time/residue: 1.0623 time to fit residues: 182.6522 Evaluate side-chains 175 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 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 332 MET 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 474 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 72 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6724 Z= 0.169 Angle : 0.613 9.859 9144 Z= 0.308 Chirality : 0.044 0.367 982 Planarity : 0.005 0.059 1173 Dihedral : 6.730 55.886 1064 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 4.32 % Allowed : 22.16 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.31), residues: 788 helix: 0.86 (0.28), residues: 376 sheet: -0.27 (0.77), residues: 42 loop : -1.47 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.018 0.001 HIS A 195 PHE 0.025 0.001 PHE A 603 TYR 0.016 0.001 TYR B 453 ARG 0.015 0.001 ARG A 559 *********************** 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 181 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 68 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7749 (mtpp) REVERT: A 156 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (mp) REVERT: A 167 SER cc_start: 0.8078 (m) cc_final: 0.7843 (p) REVERT: A 177 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7059 (ttm170) REVERT: A 189 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7245 (tp30) REVERT: A 227 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7112 (mm-30) REVERT: B 509 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7833 (mtt90) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 1.1196 time to fit residues: 192.0951 Evaluate side-chains 175 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 223 ILE 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 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 487 ASN B 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6724 Z= 0.202 Angle : 0.623 9.875 9144 Z= 0.313 Chirality : 0.045 0.363 982 Planarity : 0.005 0.060 1173 Dihedral : 6.631 55.429 1064 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.63 % Rotamer: Outliers : 4.60 % Allowed : 21.87 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.31), residues: 788 helix: 0.88 (0.28), residues: 377 sheet: -0.26 (0.78), residues: 42 loop : -1.43 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.014 0.001 HIS A 195 PHE 0.020 0.001 PHE A 592 TYR 0.016 0.001 TYR B 453 ARG 0.017 0.001 ARG A 559 *********************** 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 184 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 23 GLU cc_start: 0.6898 (mp0) cc_final: 0.6649 (mp0) REVERT: A 68 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7757 (mtpp) REVERT: A 156 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 167 SER cc_start: 0.8121 (m) cc_final: 0.7891 (p) REVERT: A 177 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7024 (ttm170) REVERT: A 189 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7260 (tp30) REVERT: A 227 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7113 (mm-30) REVERT: A 313 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6998 (ptpt) REVERT: B 509 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7708 (mtt90) outliers start: 32 outliers final: 21 residues processed: 166 average time/residue: 1.1008 time to fit residues: 193.3157 Evaluate side-chains 177 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 203 TRP 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 376 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 487 ASN B 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6724 Z= 0.177 Angle : 0.610 9.863 9144 Z= 0.306 Chirality : 0.044 0.355 982 Planarity : 0.005 0.059 1173 Dihedral : 6.447 54.189 1064 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 4.17 % Allowed : 22.59 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 788 helix: 1.06 (0.28), residues: 370 sheet: -0.25 (0.81), residues: 42 loop : -1.35 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.024 0.001 PHE A 603 TYR 0.016 0.001 TYR B 453 ARG 0.016 0.001 ARG A 559 ********************** 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 182 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 68 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7732 (mtpp) REVERT: A 156 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 167 SER cc_start: 0.8128 (m) cc_final: 0.7893 (p) REVERT: A 177 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7026 (ttm170) REVERT: A 189 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7213 (tp30) REVERT: A 227 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7101 (mm-30) REVERT: A 313 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6970 (ptpt) REVERT: B 500 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7352 (p) REVERT: B 509 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7724 (mtt90) outliers start: 29 outliers final: 20 residues processed: 164 average time/residue: 1.1138 time to fit residues: 192.4802 Evaluate side-chains 176 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE 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 471 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 195 HIS A 586 ASN B 409 GLN B 487 ASN B 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.146099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126689 restraints weight = 11218.879| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.25 r_work: 0.3557 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6724 Z= 0.207 Angle : 0.619 9.882 9144 Z= 0.311 Chirality : 0.045 0.353 982 Planarity : 0.005 0.061 1173 Dihedral : 6.409 54.597 1064 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.62 % Favored : 92.12 % Rotamer: Outliers : 3.60 % Allowed : 23.31 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 788 helix: 1.05 (0.28), residues: 370 sheet: -0.13 (0.81), residues: 41 loop : -1.35 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.002 PHE A 592 TYR 0.016 0.001 TYR B 453 ARG 0.016 0.001 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3625.96 seconds wall clock time: 63 minutes 53.03 seconds (3833.03 seconds total)