Starting phenix.real_space_refine on Sun Dec 29 09:54:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.map" model { file = "/net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eob_28333/12_2024/8eob_28333.cif" } resolution = 3.1 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= 0.969 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 6411 2.51 5 N 1701 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5053 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 2 Chain: "B" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5024 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.27, per 1000 atoms: 0.62 Number of scatterers: 10141 At special positions: 0 Unit cell: (94.696, 94.696, 130.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1975 8.00 N 1701 7.00 C 6411 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: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 46.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.857A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 60 removed outlier: 4.603A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.132A pdb=" N TYR A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.797A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 397 through 420 removed outlier: 4.146A pdb=" N LEU A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.505A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.792A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.541A pdb=" N LYS A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.338A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.517A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.882A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 60 removed outlier: 3.548A pdb=" N ILE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.545A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.614A pdb=" N THR B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 398 through 420 Processing helix chain 'B' and resid 422 through 444 removed outlier: 6.411A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.649A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 removed outlier: 4.166A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.482A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.887A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.560A pdb=" N GLY B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.739A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.780A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.745A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.712A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.507A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.059A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580 Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 323 removed outlier: 6.620A pdb=" N ILE B 335 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL B 318 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS B 320 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 331 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 322 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 329 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.896A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580 482 hydrogen bonds defined for protein. 1335 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: 3.42 Time building geometry restraints manager: 3.08 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: 3319 1.34 - 1.46: 2159 1.46 - 1.58: 4746 1.58 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 10309 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.566 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 10304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 13824 3.36 - 6.73: 43 6.73 - 10.09: 6 10.09 - 13.45: 2 13.45 - 16.81: 2 Bond angle restraints: 13877 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.14 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.34 15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.37 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 110.02 -8.97 3.00e+00 1.11e-01 8.94e+00 ... (remaining 13872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5975 17.72 - 35.44: 343 35.44 - 53.15: 59 53.15 - 70.87: 8 70.87 - 88.59: 4 Dihedral angle restraints: 6389 sinusoidal: 2728 harmonic: 3661 Sorted by residual: dihedral pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" CB LYS B 481 " pdb=" CG LYS B 481 " ideal model delta sinusoidal sigma weight residual -180.00 -125.36 -54.64 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N ASN B 150 " pdb=" CA ASN B 150 " pdb=" CB ASN B 150 " pdb=" CG ASN B 150 " ideal model delta sinusoidal sigma weight residual -60.00 -113.44 53.44 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA GLU A 368 " pdb=" CB GLU A 368 " pdb=" CG GLU A 368 " pdb=" CD GLU A 368 " ideal model delta sinusoidal sigma weight residual 60.00 111.90 -51.90 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 6386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1288 0.052 - 0.104: 213 0.104 - 0.156: 42 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1545 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1542 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 371 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP A 52 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 53 " -0.009 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 85 2.54 - 3.13: 7948 3.13 - 3.72: 15479 3.72 - 4.31: 21776 4.31 - 4.90: 37185 Nonbonded interactions: 82473 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb=" O2G ANP B 801 " model vdw 1.945 3.040 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 1.979 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 1.988 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 2.062 2.250 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.081 2.170 ... (remaining 82468 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' and (resid 11 through 220 or resid 275 through 345 or resid 351 throu \ gh 690 or resid 801 through 802)) 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=0.00 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: 0.430 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.152 10309 Z= 0.336 Angle : 0.607 16.814 13877 Z= 0.296 Chirality : 0.041 0.260 1545 Planarity : 0.003 0.043 1765 Dihedral : 11.565 88.591 4015 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 6.41 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.24), residues: 1233 helix: 1.34 (0.24), residues: 509 sheet: 0.36 (0.35), residues: 227 loop : -0.83 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 157 HIS 0.002 0.001 HIS B 458 PHE 0.009 0.001 PHE B 334 TYR 0.015 0.002 TYR A 134 ARG 0.002 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLN cc_start: 0.8811 (pm20) cc_final: 0.8581 (pm20) REVERT: A 374 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 553 MET cc_start: 0.7275 (tpp) cc_final: 0.6984 (tpp) REVERT: A 606 MET cc_start: 0.8016 (ptp) cc_final: 0.7687 (ptp) REVERT: A 607 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8389 (mttt) REVERT: A 629 ASN cc_start: 0.9296 (t0) cc_final: 0.8731 (t0) REVERT: A 636 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7378 (tm-30) REVERT: A 660 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8128 (mt-10) REVERT: B 70 GLU cc_start: 0.8044 (tt0) cc_final: 0.7730 (tt0) REVERT: B 118 GLN cc_start: 0.9042 (pp30) cc_final: 0.8560 (pp30) REVERT: B 196 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8206 (tpp80) REVERT: B 312 TRP cc_start: 0.8050 (p90) cc_final: 0.7792 (p90) REVERT: B 377 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 490 SER cc_start: 0.8974 (t) cc_final: 0.8638 (t) REVERT: B 494 VAL cc_start: 0.9299 (t) cc_final: 0.8920 (m) REVERT: B 526 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8912 (mmtm) REVERT: B 553 MET cc_start: 0.6635 (tpp) cc_final: 0.6204 (tpp) REVERT: B 581 SER cc_start: 0.8392 (t) cc_final: 0.7872 (t) REVERT: B 584 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 599 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 602 MET cc_start: 0.8438 (tpp) cc_final: 0.7973 (tpp) REVERT: B 607 LYS cc_start: 0.8692 (tppt) cc_final: 0.8360 (mmtp) outliers start: 20 outliers final: 7 residues processed: 182 average time/residue: 0.2533 time to fit residues: 63.5804 Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 ASN B 80 GLN B 447 ASN B 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 10309 Z= 0.411 Angle : 0.569 7.814 13877 Z= 0.298 Chirality : 0.044 0.161 1545 Planarity : 0.004 0.041 1765 Dihedral : 7.014 70.857 1430 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.85 % Allowed : 9.71 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.24), residues: 1233 helix: 1.69 (0.23), residues: 501 sheet: 0.16 (0.35), residues: 232 loop : -0.68 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 157 HIS 0.003 0.001 HIS A 205 PHE 0.014 0.001 PHE A 113 TYR 0.017 0.002 TYR A 426 ARG 0.007 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8669 (p90) cc_final: 0.8270 (p90) REVERT: A 374 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 465 GLU cc_start: 0.8230 (pp20) cc_final: 0.7848 (pp20) REVERT: A 549 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6156 (tm-30) REVERT: A 553 MET cc_start: 0.7360 (tpp) cc_final: 0.7076 (tpp) REVERT: A 606 MET cc_start: 0.8336 (ptp) cc_final: 0.8049 (ptp) REVERT: A 621 MET cc_start: 0.8535 (mmm) cc_final: 0.8309 (mmm) REVERT: A 629 ASN cc_start: 0.9345 (t0) cc_final: 0.8871 (t0) REVERT: A 636 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7530 (tm-30) REVERT: A 660 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8719 (mm-30) REVERT: B 70 GLU cc_start: 0.8096 (tt0) cc_final: 0.7815 (tt0) REVERT: B 118 GLN cc_start: 0.9088 (pp30) cc_final: 0.8506 (pp30) REVERT: B 312 TRP cc_start: 0.8032 (p90) cc_final: 0.7809 (p90) REVERT: B 368 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: B 377 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (mt) REVERT: B 490 SER cc_start: 0.8707 (t) cc_final: 0.7774 (p) REVERT: B 494 VAL cc_start: 0.9216 (t) cc_final: 0.8769 (m) REVERT: B 537 THR cc_start: 0.9245 (t) cc_final: 0.8993 (p) REVERT: B 553 MET cc_start: 0.6727 (tpp) cc_final: 0.6274 (tpp) REVERT: B 581 SER cc_start: 0.8562 (t) cc_final: 0.8111 (t) REVERT: B 584 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8780 (mm) REVERT: B 599 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8587 (p) REVERT: B 602 MET cc_start: 0.8491 (tpp) cc_final: 0.8003 (tpp) REVERT: B 607 LYS cc_start: 0.8487 (tppt) cc_final: 0.8234 (mttm) REVERT: B 612 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7492 (mtp180) outliers start: 32 outliers final: 14 residues processed: 139 average time/residue: 0.2180 time to fit residues: 43.5604 Evaluate side-chains 120 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10309 Z= 0.146 Angle : 0.436 4.843 13877 Z= 0.235 Chirality : 0.039 0.153 1545 Planarity : 0.003 0.040 1765 Dihedral : 5.909 65.742 1427 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 11.04 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.25), residues: 1233 helix: 2.01 (0.24), residues: 501 sheet: 0.37 (0.35), residues: 235 loop : -0.40 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.001 0.000 HIS A 632 PHE 0.007 0.001 PHE A 165 TYR 0.011 0.001 TYR B 373 ARG 0.003 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.9135 (mtm) cc_final: 0.8886 (mtp) REVERT: A 312 TRP cc_start: 0.8673 (p90) cc_final: 0.8342 (p90) REVERT: A 465 GLU cc_start: 0.8059 (pp20) cc_final: 0.7669 (pp20) REVERT: A 553 MET cc_start: 0.7327 (tpp) cc_final: 0.7035 (tpp) REVERT: A 629 ASN cc_start: 0.9275 (t0) cc_final: 0.8939 (t0) REVERT: A 636 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7500 (tm-30) REVERT: B 70 GLU cc_start: 0.8036 (tt0) cc_final: 0.7815 (tt0) REVERT: B 118 GLN cc_start: 0.9120 (pp30) cc_final: 0.8650 (pp30) REVERT: B 363 MET cc_start: 0.8677 (ptm) cc_final: 0.8452 (ptm) REVERT: B 366 CYS cc_start: 0.8089 (t) cc_final: 0.7639 (m) REVERT: B 368 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: B 372 GLU cc_start: 0.8110 (tp30) cc_final: 0.7876 (tp30) REVERT: B 375 ASN cc_start: 0.8627 (p0) cc_final: 0.8351 (p0) REVERT: B 405 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8270 (ttm-80) REVERT: B 490 SER cc_start: 0.8412 (t) cc_final: 0.7552 (p) REVERT: B 494 VAL cc_start: 0.9152 (t) cc_final: 0.8773 (m) REVERT: B 526 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8820 (mmtm) REVERT: B 553 MET cc_start: 0.7073 (tpp) cc_final: 0.6584 (tpp) REVERT: B 561 GLU cc_start: 0.8519 (pm20) cc_final: 0.7899 (pm20) REVERT: B 599 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 602 MET cc_start: 0.8241 (tpp) cc_final: 0.8012 (tpp) REVERT: B 607 LYS cc_start: 0.8574 (tppt) cc_final: 0.8316 (mttm) REVERT: B 612 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7607 (mtp180) REVERT: B 629 ASN cc_start: 0.9078 (t0) cc_final: 0.8860 (t0) REVERT: B 663 LEU cc_start: 0.8871 (tp) cc_final: 0.8566 (mp) outliers start: 20 outliers final: 9 residues processed: 144 average time/residue: 0.2308 time to fit residues: 48.2239 Evaluate side-chains 117 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10309 Z= 0.192 Angle : 0.447 4.998 13877 Z= 0.238 Chirality : 0.040 0.154 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.432 63.342 1418 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.14 % Allowed : 11.84 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.25), residues: 1233 helix: 1.97 (0.23), residues: 499 sheet: 0.36 (0.35), residues: 236 loop : -0.43 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 157 HIS 0.002 0.001 HIS B 632 PHE 0.008 0.001 PHE B 15 TYR 0.015 0.001 TYR A 211 ARG 0.002 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8681 (p90) cc_final: 0.8368 (p90) REVERT: A 465 GLU cc_start: 0.8119 (pp20) cc_final: 0.7738 (pp20) REVERT: A 553 MET cc_start: 0.7361 (tpp) cc_final: 0.7062 (tpp) REVERT: A 629 ASN cc_start: 0.9260 (t0) cc_final: 0.8990 (t0) REVERT: A 636 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7517 (tm-30) REVERT: B 70 GLU cc_start: 0.8098 (tt0) cc_final: 0.7870 (tt0) REVERT: B 118 GLN cc_start: 0.9123 (pp30) cc_final: 0.8666 (pp30) REVERT: B 363 MET cc_start: 0.8741 (ptm) cc_final: 0.8522 (ptm) REVERT: B 366 CYS cc_start: 0.8099 (t) cc_final: 0.7668 (m) REVERT: B 368 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: B 372 GLU cc_start: 0.8183 (tp30) cc_final: 0.7895 (tp30) REVERT: B 375 ASN cc_start: 0.8637 (p0) cc_final: 0.8349 (p0) REVERT: B 490 SER cc_start: 0.8446 (t) cc_final: 0.7560 (p) REVERT: B 494 VAL cc_start: 0.9168 (t) cc_final: 0.8756 (m) REVERT: B 515 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 553 MET cc_start: 0.7018 (tpp) cc_final: 0.6528 (tpp) REVERT: B 561 GLU cc_start: 0.8474 (pm20) cc_final: 0.8180 (pm20) REVERT: B 607 LYS cc_start: 0.8568 (tppt) cc_final: 0.8288 (mttm) REVERT: B 627 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 629 ASN cc_start: 0.9109 (t0) cc_final: 0.8843 (t0) outliers start: 24 outliers final: 15 residues processed: 126 average time/residue: 0.2114 time to fit residues: 39.3963 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 635 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.0010 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10309 Z= 0.145 Angle : 0.429 5.371 13877 Z= 0.228 Chirality : 0.039 0.150 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.092 58.435 1415 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.87 % Allowed : 12.64 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.25), residues: 1233 helix: 2.06 (0.23), residues: 499 sheet: 0.41 (0.34), residues: 241 loop : -0.43 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.002 0.000 HIS A 632 PHE 0.007 0.001 PHE A 165 TYR 0.011 0.001 TYR A 211 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8669 (p90) cc_final: 0.8376 (p90) REVERT: A 343 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8003 (tt) REVERT: A 465 GLU cc_start: 0.8007 (pp20) cc_final: 0.7584 (pp20) REVERT: A 553 MET cc_start: 0.7452 (tpp) cc_final: 0.7172 (tpp) REVERT: A 629 ASN cc_start: 0.9261 (t0) cc_final: 0.9044 (t0) REVERT: A 636 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7554 (tm-30) REVERT: B 70 GLU cc_start: 0.8096 (tt0) cc_final: 0.7875 (tt0) REVERT: B 118 GLN cc_start: 0.9102 (pp30) cc_final: 0.8633 (pp30) REVERT: B 363 MET cc_start: 0.8728 (ptm) cc_final: 0.8522 (ptm) REVERT: B 366 CYS cc_start: 0.8058 (t) cc_final: 0.7632 (m) REVERT: B 368 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6853 (pm20) REVERT: B 372 GLU cc_start: 0.8141 (tp30) cc_final: 0.7855 (tp30) REVERT: B 375 ASN cc_start: 0.8639 (p0) cc_final: 0.8342 (p0) REVERT: B 405 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8255 (ttm-80) REVERT: B 490 SER cc_start: 0.8432 (t) cc_final: 0.7543 (p) REVERT: B 494 VAL cc_start: 0.9152 (t) cc_final: 0.8744 (m) REVERT: B 515 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: B 553 MET cc_start: 0.7034 (tpp) cc_final: 0.6539 (tpp) REVERT: B 561 GLU cc_start: 0.8437 (pm20) cc_final: 0.8233 (pm20) REVERT: B 607 LYS cc_start: 0.8605 (tppt) cc_final: 0.8317 (mttm) REVERT: B 629 ASN cc_start: 0.9107 (t0) cc_final: 0.8834 (t0) REVERT: B 668 PHE cc_start: 0.8909 (m-80) cc_final: 0.8661 (m-80) outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 0.2175 time to fit residues: 39.6299 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10309 Z= 0.201 Angle : 0.456 6.082 13877 Z= 0.241 Chirality : 0.040 0.157 1545 Planarity : 0.003 0.036 1765 Dihedral : 5.147 55.251 1415 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.87 % Allowed : 12.73 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.25), residues: 1233 helix: 2.03 (0.23), residues: 505 sheet: 0.45 (0.34), residues: 241 loop : -0.46 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.002 0.001 HIS B 632 PHE 0.008 0.001 PHE B 15 TYR 0.012 0.001 TYR B 134 ARG 0.002 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8605 (p90) cc_final: 0.8327 (p90) REVERT: A 374 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 465 GLU cc_start: 0.8052 (pp20) cc_final: 0.7629 (pp20) REVERT: A 553 MET cc_start: 0.7346 (tpp) cc_final: 0.7032 (tpp) REVERT: A 613 ASP cc_start: 0.8309 (p0) cc_final: 0.7776 (p0) REVERT: A 629 ASN cc_start: 0.9265 (t0) cc_final: 0.9034 (t0) REVERT: A 636 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7545 (tm-30) REVERT: B 70 GLU cc_start: 0.8109 (tt0) cc_final: 0.7884 (tt0) REVERT: B 118 GLN cc_start: 0.9093 (pp30) cc_final: 0.8608 (pp30) REVERT: B 366 CYS cc_start: 0.8082 (t) cc_final: 0.7679 (m) REVERT: B 368 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: B 405 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8272 (ttm-80) REVERT: B 490 SER cc_start: 0.8453 (t) cc_final: 0.7786 (p) REVERT: B 515 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: B 553 MET cc_start: 0.6973 (tpp) cc_final: 0.6494 (tpp) REVERT: B 607 LYS cc_start: 0.8617 (tppt) cc_final: 0.8314 (mttm) REVERT: B 629 ASN cc_start: 0.9125 (t0) cc_final: 0.8833 (t0) REVERT: B 668 PHE cc_start: 0.8909 (m-80) cc_final: 0.8681 (m-80) outliers start: 21 outliers final: 15 residues processed: 122 average time/residue: 0.2169 time to fit residues: 38.6368 Evaluate side-chains 118 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10309 Z= 0.210 Angle : 0.468 6.557 13877 Z= 0.244 Chirality : 0.040 0.156 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.168 54.216 1415 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.69 % Allowed : 13.09 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.25), residues: 1233 helix: 2.05 (0.23), residues: 505 sheet: 0.45 (0.34), residues: 241 loop : -0.44 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.002 0.001 HIS B 632 PHE 0.008 0.001 PHE B 15 TYR 0.012 0.001 TYR B 134 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8609 (p90) cc_final: 0.8339 (p90) REVERT: A 343 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 374 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 465 GLU cc_start: 0.8061 (pp20) cc_final: 0.7631 (pp20) REVERT: A 553 MET cc_start: 0.7348 (tpp) cc_final: 0.7049 (tpp) REVERT: A 606 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8010 (ptp) REVERT: A 613 ASP cc_start: 0.8104 (p0) cc_final: 0.7486 (p0) REVERT: A 629 ASN cc_start: 0.9239 (t0) cc_final: 0.8997 (t0) REVERT: B 70 GLU cc_start: 0.8113 (tt0) cc_final: 0.7888 (tt0) REVERT: B 118 GLN cc_start: 0.9093 (pp30) cc_final: 0.8611 (pp30) REVERT: B 366 CYS cc_start: 0.8061 (t) cc_final: 0.7642 (m) REVERT: B 368 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: B 405 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8245 (ttm-80) REVERT: B 490 SER cc_start: 0.8425 (t) cc_final: 0.7544 (p) REVERT: B 494 VAL cc_start: 0.9180 (t) cc_final: 0.8766 (m) REVERT: B 515 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 553 MET cc_start: 0.7181 (tpp) cc_final: 0.6697 (tpp) REVERT: B 607 LYS cc_start: 0.8590 (tppt) cc_final: 0.8284 (mttm) REVERT: B 629 ASN cc_start: 0.9118 (t0) cc_final: 0.8818 (t0) REVERT: B 668 PHE cc_start: 0.8868 (m-80) cc_final: 0.8662 (m-80) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 0.2161 time to fit residues: 37.3720 Evaluate side-chains 115 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10309 Z= 0.299 Angle : 0.511 7.217 13877 Z= 0.265 Chirality : 0.041 0.160 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.358 55.263 1415 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.32 % Allowed : 13.27 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.24), residues: 1233 helix: 1.96 (0.23), residues: 504 sheet: 0.39 (0.35), residues: 231 loop : -0.52 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.003 0.001 HIS B 632 PHE 0.011 0.001 PHE B 15 TYR 0.016 0.002 TYR A 426 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8616 (p90) cc_final: 0.8343 (p90) REVERT: A 343 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 374 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8637 (mp) REVERT: A 465 GLU cc_start: 0.8134 (pp20) cc_final: 0.7694 (pp20) REVERT: A 553 MET cc_start: 0.7343 (tpp) cc_final: 0.7017 (tpp) REVERT: A 606 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7967 (ptp) REVERT: A 613 ASP cc_start: 0.8126 (p0) cc_final: 0.7428 (p0) REVERT: A 629 ASN cc_start: 0.9274 (t0) cc_final: 0.9006 (t0) REVERT: A 636 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7524 (tm-30) REVERT: B 70 GLU cc_start: 0.8130 (tt0) cc_final: 0.7897 (tt0) REVERT: B 118 GLN cc_start: 0.9097 (pp30) cc_final: 0.8724 (pp30) REVERT: B 366 CYS cc_start: 0.8075 (t) cc_final: 0.7681 (m) REVERT: B 368 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: B 490 SER cc_start: 0.8466 (t) cc_final: 0.7824 (p) REVERT: B 515 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: B 553 MET cc_start: 0.7098 (tpp) cc_final: 0.6666 (tpp) REVERT: B 602 MET cc_start: 0.8476 (tpt) cc_final: 0.8150 (tpt) REVERT: B 607 LYS cc_start: 0.8554 (tppt) cc_final: 0.8229 (mttm) outliers start: 26 outliers final: 16 residues processed: 114 average time/residue: 0.2387 time to fit residues: 40.2967 Evaluate side-chains 118 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 635 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 0.0570 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10309 Z= 0.293 Angle : 0.511 7.744 13877 Z= 0.266 Chirality : 0.041 0.160 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.380 54.566 1415 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.05 % Allowed : 13.62 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.24), residues: 1233 helix: 1.85 (0.23), residues: 510 sheet: 0.36 (0.35), residues: 231 loop : -0.57 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.002 0.001 HIS B 632 PHE 0.009 0.001 PHE B 15 TYR 0.015 0.002 TYR A 426 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8254 (t0) cc_final: 0.8043 (t0) REVERT: A 312 TRP cc_start: 0.8596 (p90) cc_final: 0.8318 (p90) REVERT: A 343 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 374 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 465 GLU cc_start: 0.8201 (pp20) cc_final: 0.7762 (pp20) REVERT: A 553 MET cc_start: 0.7296 (tpp) cc_final: 0.6963 (tpp) REVERT: A 606 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7991 (ptp) REVERT: A 613 ASP cc_start: 0.8178 (p0) cc_final: 0.7540 (p0) REVERT: A 619 TYR cc_start: 0.8701 (m-80) cc_final: 0.8353 (m-80) REVERT: A 629 ASN cc_start: 0.9275 (t0) cc_final: 0.8992 (t0) REVERT: A 636 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7512 (tm-30) REVERT: B 70 GLU cc_start: 0.8097 (tt0) cc_final: 0.7868 (tt0) REVERT: B 118 GLN cc_start: 0.9106 (pp30) cc_final: 0.8754 (pp30) REVERT: B 366 CYS cc_start: 0.8065 (t) cc_final: 0.7684 (m) REVERT: B 368 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: B 372 GLU cc_start: 0.8279 (tp30) cc_final: 0.7969 (tp30) REVERT: B 490 SER cc_start: 0.8455 (t) cc_final: 0.7587 (p) REVERT: B 494 VAL cc_start: 0.9222 (t) cc_final: 0.8808 (m) REVERT: B 515 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: B 553 MET cc_start: 0.6987 (tpp) cc_final: 0.6515 (tpp) REVERT: B 607 LYS cc_start: 0.8542 (tppt) cc_final: 0.8238 (mttm) outliers start: 23 outliers final: 18 residues processed: 114 average time/residue: 0.2061 time to fit residues: 34.6698 Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 635 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10309 Z= 0.164 Angle : 0.467 8.404 13877 Z= 0.244 Chirality : 0.039 0.155 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.099 53.525 1415 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.78 % Allowed : 13.80 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.25), residues: 1233 helix: 2.00 (0.23), residues: 505 sheet: 0.40 (0.35), residues: 236 loop : -0.45 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 157 HIS 0.001 0.000 HIS A 632 PHE 0.007 0.001 PHE B 15 TYR 0.010 0.001 TYR B 134 ARG 0.002 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8577 (p90) cc_final: 0.8316 (p90) REVERT: A 343 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 465 GLU cc_start: 0.8132 (pp20) cc_final: 0.7701 (pp20) REVERT: A 553 MET cc_start: 0.7396 (tpp) cc_final: 0.7069 (tpp) REVERT: A 573 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8380 (pttt) REVERT: A 606 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7678 (ptm) REVERT: A 613 ASP cc_start: 0.7984 (p0) cc_final: 0.7419 (p0) REVERT: A 619 TYR cc_start: 0.8677 (m-80) cc_final: 0.8332 (m-80) REVERT: A 629 ASN cc_start: 0.9245 (t0) cc_final: 0.9008 (t0) REVERT: B 70 GLU cc_start: 0.8097 (tt0) cc_final: 0.7888 (tt0) REVERT: B 118 GLN cc_start: 0.9112 (pp30) cc_final: 0.8708 (pp30) REVERT: B 366 CYS cc_start: 0.7964 (t) cc_final: 0.7583 (m) REVERT: B 368 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: B 405 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: B 490 SER cc_start: 0.8424 (t) cc_final: 0.7549 (p) REVERT: B 494 VAL cc_start: 0.9169 (t) cc_final: 0.8763 (m) REVERT: B 515 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: B 553 MET cc_start: 0.6967 (tpp) cc_final: 0.6493 (tpp) REVERT: B 561 GLU cc_start: 0.8569 (pm20) cc_final: 0.8080 (pm20) REVERT: B 607 LYS cc_start: 0.8519 (tppt) cc_final: 0.8198 (mttm) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.2413 time to fit residues: 41.3623 Evaluate side-chains 118 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077099 restraints weight = 18162.646| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.00 r_work: 0.2801 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10309 Z= 0.203 Angle : 0.483 8.403 13877 Z= 0.252 Chirality : 0.040 0.156 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.150 54.429 1415 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.78 % Allowed : 14.07 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.25), residues: 1233 helix: 1.94 (0.23), residues: 513 sheet: 0.40 (0.35), residues: 236 loop : -0.48 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 157 HIS 0.002 0.001 HIS B 632 PHE 0.008 0.001 PHE B 15 TYR 0.012 0.001 TYR A 426 ARG 0.003 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.00 seconds wall clock time: 36 minutes 56.05 seconds (2216.05 seconds total)