Starting phenix.real_space_refine on Mon Sep 23 22:11:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzv_41770/09_2024/8tzv_41770.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzv_41770/09_2024/8tzv_41770.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/8tzv_41770/09_2024/8tzv_41770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzv_41770/09_2024/8tzv_41770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzv_41770/09_2024/8tzv_41770.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzv_41770/09_2024/8tzv_41770.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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 2 6.06 5 S 44 5.16 5 C 3634 2.51 5 N 948 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2839 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322} Chain breaks: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2839 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 138 SG CYS A 23 22.992 26.367 78.483 1.00205.25 S ATOM 160 SG CYS A 26 20.287 26.051 79.798 1.00196.05 S ATOM 528 SG CYS A 71 19.264 28.175 79.875 1.00207.19 S ATOM 534 SG CYS A 72 23.034 28.417 80.130 1.00186.79 S ATOM 2977 SG CYS B 23 23.388 44.045 32.883 1.00220.55 S ATOM 2999 SG CYS B 26 21.848 44.317 31.167 1.00214.45 S ATOM 3367 SG CYS B 71 20.232 42.218 31.374 1.00209.17 S ATOM 3373 SG CYS B 72 23.292 42.074 29.559 1.00201.96 S Time building chain proxies: 3.81, per 1000 atoms: 0.67 Number of scatterers: 5680 At special positions: 0 Unit cell: (75.04, 69.68, 111.22, 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 2 29.99 S 44 16.00 O 1052 8.00 N 948 7.00 C 3634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 653.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 600 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 26 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 72 " pdb=" ZN B 600 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 26 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 23 " Number of angles added : 12 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 39.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.853A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 448 Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 482 through 487 removed outlier: 4.110A pdb=" N LYS A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 511 removed outlier: 3.793A pdb=" N GLU A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N LYS A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 53 removed outlier: 3.911A pdb=" N ASP B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 84 removed outlier: 3.652A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing helix chain 'B' and resid 87 through 104 Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.646A pdb=" N PHE B 376 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 398 removed outlier: 3.716A pdb=" N TYR B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.624A pdb=" N LEU B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 494 through 512 removed outlier: 3.901A pdb=" N VAL B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LYS B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS B 509 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.600A pdb=" N GLY A 36 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 11 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 10 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 276 removed outlier: 6.674A pdb=" N GLY A 338 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP A 357 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE A 340 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 355 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN A 342 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 353 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 344 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 367 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP A 357 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER A 365 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 removed outlier: 5.262A pdb=" N MET B 37 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 15 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA B 39 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 13 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 472 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 276 removed outlier: 4.043A pdb=" N ALA B 352 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 346 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 357 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER B 365 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 363 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 407 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 365 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N TYR B 409 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 15.313A pdb=" N TYR B 367 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 77 " --> pdb=" O MET B 406 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 408 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR B 75 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR B 76 " --> pdb=" O LEU B 428 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 600 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: 1.67 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1794 1.34 - 1.46: 1391 1.46 - 1.58: 2597 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 5842 Sorted by residual: bond pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 1.530 1.539 -0.010 1.11e-02 8.12e+03 7.34e-01 bond pdb=" CA VAL B 277 " pdb=" CB VAL B 277 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 6.65e-01 bond pdb=" CA GLY A 59 " pdb=" C GLY A 59 " ideal model delta sigma weight residual 1.514 1.523 -0.008 1.41e-02 5.03e+03 3.44e-01 bond pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 1.528 1.521 0.007 1.20e-02 6.94e+03 3.24e-01 bond pdb=" CA LEU A 442 " pdb=" C LEU A 442 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.46e-01 ... (remaining 5837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 7699 0.95 - 1.89: 137 1.89 - 2.84: 38 2.84 - 3.79: 26 3.79 - 4.74: 2 Bond angle restraints: 7902 Sorted by residual: angle pdb=" C LEU B 442 " pdb=" N PRO B 443 " pdb=" CA PRO B 443 " ideal model delta sigma weight residual 121.91 118.95 2.96 1.35e+00 5.49e-01 4.79e+00 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 106.32 109.71 -3.39 1.61e+00 3.86e-01 4.43e+00 angle pdb=" C ILE A 479 " pdb=" N MET A 480 " pdb=" CA MET A 480 " ideal model delta sigma weight residual 122.74 119.25 3.49 2.44e+00 1.68e-01 2.05e+00 angle pdb=" CA PRO A 9 " pdb=" C PRO A 9 " pdb=" N SER A 10 " ideal model delta sigma weight residual 114.75 116.68 -1.93 1.45e+00 4.76e-01 1.78e+00 angle pdb=" C ARG A 423 " pdb=" CA ARG A 423 " pdb=" CB ARG A 423 " ideal model delta sigma weight residual 108.91 111.01 -2.10 1.65e+00 3.67e-01 1.62e+00 ... (remaining 7897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.83: 3279 10.83 - 21.66: 186 21.66 - 32.49: 51 32.49 - 43.32: 13 43.32 - 54.15: 3 Dihedral angle restraints: 3532 sinusoidal: 1466 harmonic: 2066 Sorted by residual: dihedral pdb=" N TYR A 485 " pdb=" CA TYR A 485 " pdb=" CB TYR A 485 " pdb=" CG TYR A 485 " ideal model delta sinusoidal sigma weight residual 60.00 114.15 -54.15 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" N ARG A 33 " pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " ideal model delta sinusoidal sigma weight residual -180.00 -127.29 -52.71 3 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -180.00 -134.43 -45.57 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 434 0.025 - 0.050: 233 0.050 - 0.074: 73 0.074 - 0.099: 39 0.099 - 0.124: 23 Chirality restraints: 802 Sorted by residual: chirality pdb=" CA ILE A 479 " pdb=" N ILE A 479 " pdb=" C ILE A 479 " pdb=" CB ILE A 479 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE B 479 " pdb=" N ILE B 479 " pdb=" C ILE B 479 " pdb=" CB ILE B 479 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL A 62 " pdb=" N VAL A 62 " pdb=" C VAL A 62 " pdb=" CB VAL A 62 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 799 not shown) Planarity restraints: 1024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 442 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 443 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 456 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 457 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 491 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.36e-01 pdb=" N PRO B 492 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 492 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 492 " -0.013 5.00e-02 4.00e+02 ... (remaining 1021 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 350 2.74 - 3.28: 5618 3.28 - 3.82: 9529 3.82 - 4.36: 11107 4.36 - 4.90: 19281 Nonbonded interactions: 45885 Sorted by model distance: nonbonded pdb=" OE1 GLU A 387 " pdb=" OH TYR A 404 " model vdw 2.199 3.040 nonbonded pdb=" OE1 GLU B 387 " pdb=" OH TYR B 404 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP B 491 " pdb=" OG SER B 493 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP A 52 " pdb=" OH TYR A 405 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP B 52 " pdb=" OH TYR B 405 " model vdw 2.254 3.040 ... (remaining 45880 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.001 0.015 5842 Z= 0.088 Angle : 0.401 4.736 7902 Z= 0.207 Chirality : 0.039 0.124 802 Planarity : 0.003 0.032 1024 Dihedral : 7.771 54.148 2212 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.47 % Allowed : 2.04 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.32), residues: 688 helix: 0.69 (0.37), residues: 236 sheet: -0.23 (0.51), residues: 110 loop : -0.19 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.003 0.000 HIS B 395 PHE 0.006 0.001 PHE B 390 TYR 0.007 0.001 TYR B 369 ARG 0.001 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.7276 (m110) cc_final: 0.5984 (m-40) REVERT: A 50 LEU cc_start: 0.8162 (mt) cc_final: 0.7941 (mp) REVERT: A 60 LYS cc_start: 0.8420 (mttm) cc_final: 0.7948 (mtpp) REVERT: A 69 GLN cc_start: 0.8706 (mt0) cc_final: 0.8367 (tp40) REVERT: A 92 LYS cc_start: 0.8121 (mttm) cc_final: 0.7884 (ptmt) REVERT: A 281 ASP cc_start: 0.7399 (t0) cc_final: 0.7177 (t70) REVERT: A 466 THR cc_start: 0.9333 (p) cc_final: 0.8979 (t) REVERT: A 467 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 470 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8210 (mmm-85) REVERT: A 495 GLU cc_start: 0.8969 (tt0) cc_final: 0.8721 (tm-30) REVERT: A 513 MET cc_start: 0.7586 (mtm) cc_final: 0.7373 (mtm) REVERT: B 13 ASP cc_start: 0.8350 (t0) cc_final: 0.7746 (t0) REVERT: B 74 GLN cc_start: 0.8789 (mt0) cc_final: 0.8574 (mt0) REVERT: B 92 LYS cc_start: 0.9135 (tttt) cc_final: 0.8370 (ttpp) REVERT: B 99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8810 (tptp) REVERT: B 103 LYS cc_start: 0.8860 (mttm) cc_final: 0.8570 (tmmt) REVERT: B 270 LEU cc_start: 0.8563 (tp) cc_final: 0.8299 (tm) REVERT: B 271 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7680 (mm-30) REVERT: B 317 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7114 (tmt-80) REVERT: B 325 GLU cc_start: 0.8328 (tt0) cc_final: 0.8099 (mm-30) REVERT: B 416 MET cc_start: 0.8711 (mmt) cc_final: 0.8296 (mmp) REVERT: B 500 GLN cc_start: 0.8638 (mt0) cc_final: 0.8287 (tp-100) outliers start: 3 outliers final: 1 residues processed: 203 average time/residue: 1.1406 time to fit residues: 241.8348 Evaluate side-chains 111 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 40 HIS A 83 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 489 GLN B 35 ASN B 304 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN B 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5842 Z= 0.215 Angle : 0.658 11.821 7902 Z= 0.323 Chirality : 0.045 0.161 802 Planarity : 0.005 0.050 1024 Dihedral : 4.016 57.192 784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.83 % Allowed : 14.15 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.00 (0.32), residues: 688 helix: 0.55 (0.35), residues: 232 sheet: -0.07 (0.53), residues: 108 loop : -0.24 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 55 HIS 0.007 0.001 HIS B 395 PHE 0.016 0.002 PHE B 292 TYR 0.018 0.001 TYR A 404 ARG 0.007 0.001 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8183 (mt) cc_final: 0.7923 (mp) REVERT: A 60 LYS cc_start: 0.8569 (mttm) cc_final: 0.8132 (mtpp) REVERT: A 92 LYS cc_start: 0.8327 (mttm) cc_final: 0.7781 (ptmt) REVERT: A 99 LYS cc_start: 0.8492 (tptp) cc_final: 0.8189 (mmmm) REVERT: A 400 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8455 (tp-100) REVERT: A 416 MET cc_start: 0.8823 (ppp) cc_final: 0.8293 (ppp) REVERT: A 418 TYR cc_start: 0.7881 (p90) cc_final: 0.7592 (p90) REVERT: A 419 LYS cc_start: 0.8616 (mttt) cc_final: 0.8169 (ptpp) REVERT: A 466 THR cc_start: 0.9316 (p) cc_final: 0.8820 (t) REVERT: A 467 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8411 (mm-30) REVERT: A 470 ARG cc_start: 0.8764 (mmt180) cc_final: 0.8422 (mmm-85) REVERT: B 13 ASP cc_start: 0.8382 (t0) cc_final: 0.8098 (t0) REVERT: B 60 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7883 (mmmm) REVERT: B 92 LYS cc_start: 0.8945 (tttt) cc_final: 0.8382 (ttpp) REVERT: B 99 LYS cc_start: 0.9054 (tppt) cc_final: 0.8797 (tptp) REVERT: B 103 LYS cc_start: 0.8831 (mttm) cc_final: 0.8631 (tptp) REVERT: B 270 LEU cc_start: 0.8596 (tp) cc_final: 0.8175 (tm) REVERT: B 271 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7576 (mm-30) REVERT: B 325 GLU cc_start: 0.8434 (tt0) cc_final: 0.8132 (mm-30) REVERT: B 416 MET cc_start: 0.8634 (mmt) cc_final: 0.8172 (mmp) REVERT: B 480 MET cc_start: 0.7643 (ptp) cc_final: 0.7410 (ptp) outliers start: 18 outliers final: 6 residues processed: 119 average time/residue: 1.1777 time to fit residues: 146.3413 Evaluate side-chains 91 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 342 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5842 Z= 0.197 Angle : 0.619 10.452 7902 Z= 0.303 Chirality : 0.047 0.401 802 Planarity : 0.004 0.036 1024 Dihedral : 4.028 56.220 784 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.62 % Allowed : 13.52 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.11 (0.32), residues: 688 helix: 0.50 (0.36), residues: 234 sheet: -0.20 (0.49), residues: 118 loop : -0.31 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 55 HIS 0.007 0.001 HIS B 341 PHE 0.014 0.001 PHE A 408 TYR 0.014 0.001 TYR A 382 ARG 0.004 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8389 (t0) cc_final: 0.8100 (t0) REVERT: A 38 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.7268 (t-100) REVERT: A 50 LEU cc_start: 0.8043 (mt) cc_final: 0.7792 (mp) REVERT: A 60 LYS cc_start: 0.8593 (mttm) cc_final: 0.8210 (mtpt) REVERT: A 92 LYS cc_start: 0.8214 (mttm) cc_final: 0.7629 (ttpp) REVERT: A 400 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8497 (tp-100) REVERT: A 464 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8236 (ptm-80) REVERT: A 466 THR cc_start: 0.9337 (p) cc_final: 0.8821 (t) REVERT: A 467 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 470 ARG cc_start: 0.8774 (mmt180) cc_final: 0.8341 (mmm-85) REVERT: A 495 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: A 499 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8608 (mp) REVERT: B 13 ASP cc_start: 0.8450 (t0) cc_final: 0.8112 (t0) REVERT: B 60 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7969 (mmmm) REVERT: B 92 LYS cc_start: 0.9053 (tttt) cc_final: 0.8726 (ptmm) REVERT: B 99 LYS cc_start: 0.9043 (tppt) cc_final: 0.8786 (tptp) REVERT: B 103 LYS cc_start: 0.8886 (mttm) cc_final: 0.8662 (tptp) REVERT: B 270 LEU cc_start: 0.8554 (tp) cc_final: 0.8197 (tm) REVERT: B 325 GLU cc_start: 0.8454 (tt0) cc_final: 0.8168 (mm-30) REVERT: B 416 MET cc_start: 0.8682 (mmt) cc_final: 0.8225 (mmp) REVERT: B 433 TYR cc_start: 0.8095 (m-80) cc_final: 0.7735 (m-80) REVERT: B 477 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7031 (ttp-110) outliers start: 23 outliers final: 8 residues processed: 102 average time/residue: 1.0226 time to fit residues: 110.0030 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 41 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5842 Z= 0.151 Angle : 0.578 9.046 7902 Z= 0.284 Chirality : 0.045 0.250 802 Planarity : 0.004 0.036 1024 Dihedral : 3.458 14.897 782 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.14 % Allowed : 13.99 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.08 (0.32), residues: 688 helix: 0.54 (0.36), residues: 234 sheet: -0.22 (0.49), residues: 118 loop : -0.31 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.005 0.001 HIS B 341 PHE 0.015 0.001 PHE A 408 TYR 0.014 0.001 TYR A 485 ARG 0.002 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7429 (OUTLIER) cc_final: 0.6964 (t-100) REVERT: A 50 LEU cc_start: 0.8080 (mt) cc_final: 0.7827 (mp) REVERT: A 60 LYS cc_start: 0.8552 (mttm) cc_final: 0.8181 (mtpt) REVERT: A 64 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7236 (ttpp) REVERT: A 67 MET cc_start: 0.8564 (mmt) cc_final: 0.8195 (mmt) REVERT: A 92 LYS cc_start: 0.8156 (mttm) cc_final: 0.7803 (ptmt) REVERT: A 99 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8481 (mmtm) REVERT: A 464 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8304 (ptm-80) REVERT: A 466 THR cc_start: 0.9348 (p) cc_final: 0.8798 (t) REVERT: A 467 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8417 (mm-30) REVERT: A 470 ARG cc_start: 0.8758 (mmt180) cc_final: 0.8451 (mmm160) REVERT: A 495 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: A 499 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8585 (mp) REVERT: B 11 VAL cc_start: 0.8809 (t) cc_final: 0.8531 (p) REVERT: B 60 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7958 (mmmm) REVERT: B 92 LYS cc_start: 0.9054 (tttt) cc_final: 0.8534 (ptmm) REVERT: B 99 LYS cc_start: 0.9038 (tppt) cc_final: 0.8821 (tptp) REVERT: B 103 LYS cc_start: 0.8893 (mttm) cc_final: 0.8627 (tptp) REVERT: B 273 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6539 (mpt-90) REVERT: B 325 GLU cc_start: 0.8420 (tt0) cc_final: 0.8160 (mm-30) REVERT: B 392 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7423 (ttm170) REVERT: B 406 MET cc_start: 0.7338 (mmm) cc_final: 0.7049 (mmm) REVERT: B 416 MET cc_start: 0.8687 (mmt) cc_final: 0.8252 (mmp) REVERT: B 477 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7158 (ttt-90) outliers start: 20 outliers final: 5 residues processed: 105 average time/residue: 1.1225 time to fit residues: 123.8694 Evaluate side-chains 90 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 303 HIS ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5842 Z= 0.294 Angle : 0.647 8.414 7902 Z= 0.322 Chirality : 0.048 0.284 802 Planarity : 0.004 0.050 1024 Dihedral : 3.662 17.819 782 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.62 % Allowed : 14.94 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.14 (0.32), residues: 688 helix: 0.50 (0.36), residues: 228 sheet: -0.49 (0.50), residues: 118 loop : -0.22 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 55 HIS 0.006 0.001 HIS B 341 PHE 0.033 0.002 PHE B 15 TYR 0.026 0.002 TYR A 485 ARG 0.003 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8121 (mt) cc_final: 0.7809 (mp) REVERT: A 60 LYS cc_start: 0.8586 (mttm) cc_final: 0.8276 (mtpp) REVERT: A 64 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7249 (ttpp) REVERT: A 353 VAL cc_start: 0.8550 (t) cc_final: 0.8271 (t) REVERT: A 466 THR cc_start: 0.9408 (p) cc_final: 0.9106 (t) REVERT: A 467 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8659 (mm-30) REVERT: A 480 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6378 (pp-130) REVERT: A 495 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: A 499 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 13 ASP cc_start: 0.8132 (t0) cc_final: 0.7914 (t0) REVERT: B 60 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8000 (mmmm) REVERT: B 92 LYS cc_start: 0.9100 (tttt) cc_final: 0.8741 (ptmm) REVERT: B 97 MET cc_start: 0.8541 (tmm) cc_final: 0.8332 (tmm) REVERT: B 99 LYS cc_start: 0.9074 (tppt) cc_final: 0.8820 (tptp) REVERT: B 103 LYS cc_start: 0.8967 (mttm) cc_final: 0.8746 (tptp) REVERT: B 273 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6753 (mpt-90) REVERT: B 281 ASP cc_start: 0.7774 (t70) cc_final: 0.7484 (t70) REVERT: B 325 GLU cc_start: 0.8528 (tt0) cc_final: 0.8194 (mp0) REVERT: B 406 MET cc_start: 0.7657 (mmm) cc_final: 0.7349 (mmm) REVERT: B 416 MET cc_start: 0.8751 (mmt) cc_final: 0.8265 (mmp) REVERT: B 477 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7209 (ttt-90) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 1.0945 time to fit residues: 107.0073 Evaluate side-chains 90 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 518 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5842 Z= 0.181 Angle : 0.610 9.380 7902 Z= 0.301 Chirality : 0.045 0.215 802 Planarity : 0.004 0.048 1024 Dihedral : 3.610 18.239 782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.30 % Allowed : 16.04 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.23 (0.32), residues: 688 helix: 0.47 (0.36), residues: 234 sheet: -0.54 (0.49), residues: 118 loop : -0.33 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 55 HIS 0.004 0.001 HIS B 341 PHE 0.014 0.001 PHE A 408 TYR 0.017 0.001 TYR A 485 ARG 0.009 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6916 (m-90) REVERT: A 50 LEU cc_start: 0.8182 (mt) cc_final: 0.7930 (mp) REVERT: A 60 LYS cc_start: 0.8607 (mttm) cc_final: 0.7955 (tttt) REVERT: A 466 THR cc_start: 0.9401 (p) cc_final: 0.9131 (t) REVERT: A 467 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 480 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6799 (ppp) REVERT: A 495 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: A 499 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 60 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7976 (mmmm) REVERT: B 92 LYS cc_start: 0.9103 (tttt) cc_final: 0.8778 (ptmm) REVERT: B 99 LYS cc_start: 0.9074 (tppt) cc_final: 0.8820 (tptp) REVERT: B 103 LYS cc_start: 0.8988 (mttm) cc_final: 0.8756 (tptp) REVERT: B 273 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6613 (mpt-90) REVERT: B 281 ASP cc_start: 0.7785 (t70) cc_final: 0.7445 (t70) REVERT: B 325 GLU cc_start: 0.8512 (tt0) cc_final: 0.8163 (mm-30) REVERT: B 396 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 406 MET cc_start: 0.7310 (mmm) cc_final: 0.6972 (mmm) REVERT: B 416 MET cc_start: 0.8741 (mmt) cc_final: 0.8266 (mmp) REVERT: B 477 ARG cc_start: 0.7593 (mtm110) cc_final: 0.6974 (ttt-90) outliers start: 21 outliers final: 7 residues processed: 92 average time/residue: 1.0035 time to fit residues: 97.4377 Evaluate side-chains 89 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 19 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5842 Z= 0.180 Angle : 0.642 11.619 7902 Z= 0.313 Chirality : 0.047 0.336 802 Planarity : 0.004 0.048 1024 Dihedral : 3.658 21.559 782 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.83 % Allowed : 16.67 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.21 (0.32), residues: 688 helix: 0.43 (0.35), residues: 234 sheet: -0.11 (0.52), residues: 102 loop : -0.45 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 38 HIS 0.003 0.001 HIS B 341 PHE 0.011 0.001 PHE A 408 TYR 0.013 0.001 TYR A 370 ARG 0.007 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7042 (m-90) REVERT: A 50 LEU cc_start: 0.8190 (mt) cc_final: 0.7878 (mt) REVERT: A 60 LYS cc_start: 0.8561 (mttm) cc_final: 0.7988 (tttp) REVERT: A 99 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8514 (mmtp) REVERT: A 325 GLU cc_start: 0.8123 (mp0) cc_final: 0.7748 (mp0) REVERT: A 466 THR cc_start: 0.9381 (p) cc_final: 0.9057 (t) REVERT: A 467 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8630 (mm-30) REVERT: A 495 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 499 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 60 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7978 (mmmm) REVERT: B 92 LYS cc_start: 0.9148 (tttt) cc_final: 0.8834 (ptmm) REVERT: B 99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8815 (tptp) REVERT: B 103 LYS cc_start: 0.8998 (mttm) cc_final: 0.8764 (tptp) REVERT: B 273 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6599 (mpt-90) REVERT: B 281 ASP cc_start: 0.7858 (t70) cc_final: 0.7532 (t70) REVERT: B 325 GLU cc_start: 0.8511 (tt0) cc_final: 0.8195 (mm-30) REVERT: B 396 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 406 MET cc_start: 0.7352 (mmm) cc_final: 0.7040 (mmm) REVERT: B 410 ILE cc_start: 0.8031 (mm) cc_final: 0.7819 (mm) REVERT: B 416 MET cc_start: 0.8733 (mmt) cc_final: 0.8286 (mmp) outliers start: 18 outliers final: 6 residues processed: 91 average time/residue: 0.9932 time to fit residues: 95.5250 Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5842 Z= 0.288 Angle : 0.690 11.236 7902 Z= 0.338 Chirality : 0.048 0.258 802 Planarity : 0.004 0.050 1024 Dihedral : 3.861 21.300 782 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.30 % Allowed : 16.51 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.32), residues: 688 helix: 0.29 (0.35), residues: 234 sheet: -0.61 (0.52), residues: 108 loop : -0.36 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 55 HIS 0.004 0.001 HIS B 395 PHE 0.015 0.002 PHE A 408 TYR 0.028 0.002 TYR A 485 ARG 0.005 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.6753 (m-80) cc_final: 0.6537 (m-80) REVERT: A 38 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6825 (t-100) REVERT: A 50 LEU cc_start: 0.8264 (mt) cc_final: 0.7900 (mt) REVERT: A 60 LYS cc_start: 0.8456 (mttm) cc_final: 0.8120 (mtpt) REVERT: A 353 VAL cc_start: 0.8528 (t) cc_final: 0.8201 (t) REVERT: A 433 TYR cc_start: 0.7831 (m-80) cc_final: 0.7416 (m-80) REVERT: A 466 THR cc_start: 0.9389 (p) cc_final: 0.9166 (t) REVERT: A 467 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8808 (mm-30) REVERT: A 480 MET cc_start: 0.6810 (ppp) cc_final: 0.6331 (pp-130) REVERT: A 495 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: A 499 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8621 (mp) REVERT: B 60 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7963 (mmmm) REVERT: B 92 LYS cc_start: 0.9220 (tttt) cc_final: 0.8859 (ptmm) REVERT: B 99 LYS cc_start: 0.9126 (tppt) cc_final: 0.8845 (tptp) REVERT: B 273 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6815 (mpt-90) REVERT: B 325 GLU cc_start: 0.8639 (tt0) cc_final: 0.8198 (mp0) REVERT: B 396 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 406 MET cc_start: 0.7430 (mmm) cc_final: 0.7129 (mmm) REVERT: B 416 MET cc_start: 0.8745 (mmt) cc_final: 0.8270 (mmp) outliers start: 21 outliers final: 9 residues processed: 84 average time/residue: 1.0813 time to fit residues: 95.6436 Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5842 Z= 0.225 Angle : 0.682 12.433 7902 Z= 0.336 Chirality : 0.047 0.245 802 Planarity : 0.004 0.050 1024 Dihedral : 3.891 21.756 782 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.20 % Allowed : 18.24 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.32), residues: 688 helix: 0.38 (0.35), residues: 234 sheet: -0.08 (0.56), residues: 90 loop : -0.45 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 38 HIS 0.005 0.001 HIS B 341 PHE 0.025 0.002 PHE B 516 TYR 0.025 0.001 TYR A 485 ARG 0.005 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8243 (mt) cc_final: 0.7881 (mt) REVERT: A 419 LYS cc_start: 0.8527 (mttt) cc_final: 0.8126 (mtmm) REVERT: A 466 THR cc_start: 0.9392 (p) cc_final: 0.9126 (t) REVERT: A 467 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8753 (mm-30) REVERT: A 480 MET cc_start: 0.7124 (ppp) cc_final: 0.6645 (pp-130) REVERT: A 495 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: A 499 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 60 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7919 (mmmm) REVERT: B 92 LYS cc_start: 0.9221 (tttt) cc_final: 0.8858 (ptmm) REVERT: B 99 LYS cc_start: 0.9170 (tppt) cc_final: 0.8878 (tptp) REVERT: B 273 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6724 (mpt-90) REVERT: B 281 ASP cc_start: 0.7857 (t70) cc_final: 0.7505 (t70) REVERT: B 325 GLU cc_start: 0.8635 (tt0) cc_final: 0.8200 (mp0) REVERT: B 396 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 406 MET cc_start: 0.7523 (mmm) cc_final: 0.7220 (mmm) REVERT: B 416 MET cc_start: 0.8820 (mmt) cc_final: 0.8400 (mmp) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 1.0460 time to fit residues: 93.7154 Evaluate side-chains 84 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.0870 chunk 62 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5842 Z= 0.183 Angle : 0.695 11.205 7902 Z= 0.332 Chirality : 0.047 0.277 802 Planarity : 0.004 0.049 1024 Dihedral : 3.889 21.598 782 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.04 % Allowed : 18.87 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 688 helix: 0.49 (0.36), residues: 234 sheet: -0.21 (0.55), residues: 90 loop : -0.35 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 38 HIS 0.003 0.001 HIS B 395 PHE 0.017 0.001 PHE B 516 TYR 0.024 0.001 TYR A 485 ARG 0.005 0.000 ARG A 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7140 (OUTLIER) cc_final: 0.6789 (m-90) REVERT: A 50 LEU cc_start: 0.8198 (mt) cc_final: 0.7832 (mt) REVERT: A 60 LYS cc_start: 0.8386 (mtpm) cc_final: 0.7795 (tttt) REVERT: A 325 GLU cc_start: 0.8064 (mp0) cc_final: 0.7741 (tp30) REVERT: A 419 LYS cc_start: 0.8500 (mttt) cc_final: 0.8256 (mtpm) REVERT: A 466 THR cc_start: 0.9392 (p) cc_final: 0.9007 (t) REVERT: A 467 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8658 (mm-30) REVERT: A 480 MET cc_start: 0.7034 (ppp) cc_final: 0.6404 (pp-130) REVERT: A 495 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: A 499 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8616 (mp) REVERT: B 60 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7977 (mmmm) REVERT: B 92 LYS cc_start: 0.9214 (tttt) cc_final: 0.8936 (ptmm) REVERT: B 99 LYS cc_start: 0.9125 (tppt) cc_final: 0.8842 (tptp) REVERT: B 273 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6610 (mpt-90) REVERT: B 281 ASP cc_start: 0.7782 (t70) cc_final: 0.7440 (t70) REVERT: B 325 GLU cc_start: 0.8613 (tt0) cc_final: 0.8287 (mp0) REVERT: B 406 MET cc_start: 0.7425 (mmm) cc_final: 0.7090 (mmm) REVERT: B 410 ILE cc_start: 0.7763 (mm) cc_final: 0.7444 (tp) REVERT: B 416 MET cc_start: 0.8710 (mmt) cc_final: 0.8323 (mmp) outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 0.9203 time to fit residues: 83.9886 Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.096714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.081983 restraints weight = 13380.909| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 4.07 r_work: 0.3580 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5842 Z= 0.197 Angle : 0.694 10.647 7902 Z= 0.333 Chirality : 0.047 0.233 802 Planarity : 0.004 0.049 1024 Dihedral : 3.853 21.326 782 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 19.65 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.32), residues: 688 helix: 0.55 (0.36), residues: 234 sheet: -0.02 (0.56), residues: 88 loop : -0.36 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 38 HIS 0.005 0.001 HIS B 341 PHE 0.018 0.001 PHE B 516 TYR 0.022 0.001 TYR A 485 ARG 0.005 0.000 ARG A 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.22 seconds wall clock time: 45 minutes 7.30 seconds (2707.30 seconds total)