Starting phenix.real_space_refine on Thu May 1 05:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eob_28333/05_2025/8eob_28333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eob_28333/05_2025/8eob_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_28333/05_2025/8eob_28333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eob_28333/05_2025/8eob_28333.map" model { file = "/net/cci-nas-00/data/ceres_data/8eob_28333/05_2025/8eob_28333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eob_28333/05_2025/8eob_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-5669/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: 6.35, per 1000 atoms: 0.63 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 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: 1.28 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: 3.54 Time building geometry restraints manager: 2.89 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: 0.470 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.370 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- 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= 0.236 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 Details of bonding type rmsd hydrogen bonds : bond 0.13827 ( 482) hydrogen bonds : angle 6.26189 ( 1335) covalent geometry : bond 0.00501 (10309) covalent geometry : angle 0.60676 (13877) *********************** 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 : 1.294 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: 0.2494 time to fit residues: 62.8078 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 : 1.130 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.074389 restraints weight = 18463.379| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.06 r_work: 0.2773 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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= 0.266 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 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 482) hydrogen bonds : angle 4.71265 ( 1335) covalent geometry : bond 0.00635 (10309) covalent geometry : angle 0.56882 (13877) *********************** 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 : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8742 (p90) cc_final: 0.8356 (p90) REVERT: A 374 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8675 (mp) REVERT: A 465 GLU cc_start: 0.8181 (pp20) cc_final: 0.7813 (pp20) REVERT: A 549 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6143 (tm-30) REVERT: A 553 MET cc_start: 0.7424 (tpp) cc_final: 0.7118 (tpp) REVERT: A 606 MET cc_start: 0.8441 (ptp) cc_final: 0.8160 (ptp) REVERT: A 621 MET cc_start: 0.8651 (mmm) cc_final: 0.8443 (mmm) REVERT: A 629 ASN cc_start: 0.9342 (t0) cc_final: 0.8860 (t0) REVERT: A 636 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7603 (tm-30) REVERT: A 660 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8750 (mm-30) REVERT: B 70 GLU cc_start: 0.8118 (tt0) cc_final: 0.7840 (tt0) REVERT: B 118 GLN cc_start: 0.9115 (pp30) cc_final: 0.8550 (pp30) REVERT: B 312 TRP cc_start: 0.8115 (p90) cc_final: 0.7895 (p90) REVERT: B 368 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: B 377 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 490 SER cc_start: 0.8760 (t) cc_final: 0.7855 (p) REVERT: B 494 VAL cc_start: 0.9270 (t) cc_final: 0.8828 (m) REVERT: B 537 THR cc_start: 0.9216 (t) cc_final: 0.8942 (p) REVERT: B 553 MET cc_start: 0.6667 (tpp) cc_final: 0.6216 (tpp) REVERT: B 581 SER cc_start: 0.8519 (t) cc_final: 0.8088 (t) REVERT: B 599 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 602 MET cc_start: 0.8611 (tpp) cc_final: 0.8156 (tpp) REVERT: B 607 LYS cc_start: 0.8639 (tppt) cc_final: 0.8387 (mttm) REVERT: B 612 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7578 (mtp180) outliers start: 32 outliers final: 14 residues processed: 139 average time/residue: 0.2095 time to fit residues: 42.6895 Evaluate side-chains 120 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076861 restraints weight = 18355.793| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.91 r_work: 0.2810 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10309 Z= 0.112 Angle : 0.448 5.213 13877 Z= 0.240 Chirality : 0.040 0.153 1545 Planarity : 0.003 0.039 1765 Dihedral : 6.047 67.279 1425 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 1.03 (0.25), residues: 1233 helix: 1.97 (0.24), residues: 500 sheet: 0.33 (0.35), residues: 230 loop : -0.43 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 B 373 ARG 0.003 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 482) hydrogen bonds : angle 4.28265 ( 1335) covalent geometry : bond 0.00257 (10309) covalent geometry : angle 0.44768 (13877) *********************** 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 144 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.9043 (mtm) cc_final: 0.8799 (mtp) REVERT: A 312 TRP cc_start: 0.8744 (p90) cc_final: 0.8419 (p90) REVERT: A 465 GLU cc_start: 0.8085 (pp20) cc_final: 0.7717 (pp20) REVERT: A 553 MET cc_start: 0.7371 (tpp) cc_final: 0.7047 (tpp) REVERT: A 629 ASN cc_start: 0.9299 (t0) cc_final: 0.8845 (t0) REVERT: A 636 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7546 (tm-30) REVERT: B 70 GLU cc_start: 0.8077 (tt0) cc_final: 0.7829 (tt0) REVERT: B 118 GLN cc_start: 0.9121 (pp30) cc_final: 0.8669 (pp30) REVERT: B 363 MET cc_start: 0.8715 (ptm) cc_final: 0.8505 (ptm) REVERT: B 366 CYS cc_start: 0.8165 (t) cc_final: 0.7756 (m) REVERT: B 368 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: B 372 GLU cc_start: 0.8164 (tp30) cc_final: 0.7920 (tp30) REVERT: B 375 ASN cc_start: 0.8588 (p0) cc_final: 0.8299 (p0) REVERT: B 490 SER cc_start: 0.8456 (t) cc_final: 0.7612 (p) REVERT: B 494 VAL cc_start: 0.9201 (t) cc_final: 0.8822 (m) REVERT: B 526 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8852 (mmtm) REVERT: B 545 GLU cc_start: 0.7689 (pm20) cc_final: 0.7446 (pm20) REVERT: B 546 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5691 (p0) REVERT: B 553 MET cc_start: 0.6913 (tpp) cc_final: 0.6403 (tpp) REVERT: B 561 GLU cc_start: 0.8489 (pm20) cc_final: 0.7905 (pm20) REVERT: B 602 MET cc_start: 0.8366 (tpp) cc_final: 0.8145 (tpp) REVERT: B 607 LYS cc_start: 0.8676 (tppt) cc_final: 0.8422 (mttm) REVERT: B 612 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7627 (mtp180) REVERT: B 629 ASN cc_start: 0.9064 (t0) cc_final: 0.8816 (t0) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 0.2118 time to fit residues: 43.8786 Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.101330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.078679 restraints weight = 18033.724| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.91 r_work: 0.2834 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10309 Z= 0.093 Angle : 0.429 5.149 13877 Z= 0.229 Chirality : 0.039 0.149 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.253 63.117 1417 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.05 % Allowed : 11.31 % Favored : 86.64 % 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 (0.24), residues: 500 sheet: 0.39 (0.35), residues: 230 loop : -0.41 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.002 0.000 HIS A 632 PHE 0.006 0.001 PHE A 165 TYR 0.010 0.001 TYR B 373 ARG 0.002 0.000 ARG A 450 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 482) hydrogen bonds : angle 4.08942 ( 1335) covalent geometry : bond 0.00211 (10309) covalent geometry : angle 0.42883 (13877) *********************** 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 137 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.9064 (mtm) cc_final: 0.8844 (mtp) REVERT: A 312 TRP cc_start: 0.8732 (p90) cc_final: 0.8446 (p90) REVERT: A 465 GLU cc_start: 0.7967 (pp20) cc_final: 0.7578 (pp20) REVERT: A 553 MET cc_start: 0.7420 (tpp) cc_final: 0.7101 (tpp) REVERT: A 572 ASP cc_start: 0.8316 (t0) cc_final: 0.8093 (m-30) REVERT: A 629 ASN cc_start: 0.9254 (t0) cc_final: 0.8975 (t0) REVERT: B 70 GLU cc_start: 0.8076 (tt0) cc_final: 0.7846 (tt0) REVERT: B 118 GLN cc_start: 0.9089 (pp30) cc_final: 0.8655 (pp30) REVERT: B 366 CYS cc_start: 0.8130 (t) cc_final: 0.7748 (m) REVERT: B 368 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: B 372 GLU cc_start: 0.8197 (tp30) cc_final: 0.7910 (tp30) REVERT: B 375 ASN cc_start: 0.8588 (p0) cc_final: 0.8291 (p0) REVERT: B 405 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8495 (ttm-80) REVERT: B 490 SER cc_start: 0.8478 (t) cc_final: 0.7608 (p) REVERT: B 494 VAL cc_start: 0.9216 (t) cc_final: 0.8821 (m) REVERT: B 515 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: B 526 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8846 (mmtm) REVERT: B 553 MET cc_start: 0.6837 (tpp) cc_final: 0.6390 (tpp) REVERT: B 561 GLU cc_start: 0.8418 (pm20) cc_final: 0.8103 (pm20) REVERT: B 607 LYS cc_start: 0.8719 (tppt) cc_final: 0.8452 (mttm) REVERT: B 629 ASN cc_start: 0.9106 (t0) cc_final: 0.8835 (t0) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 0.2202 time to fit residues: 42.0902 Evaluate side-chains 117 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 670 LEU Chi-restraints excluded: chain A residue 678 ASN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 0.9864 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.100529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.079044 restraints weight = 18126.756| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.82 r_work: 0.2838 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10309 Z= 0.098 Angle : 0.428 5.692 13877 Z= 0.227 Chirality : 0.039 0.150 1545 Planarity : 0.003 0.036 1765 Dihedral : 5.093 59.382 1415 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.96 % Allowed : 12.20 % Favored : 85.84 % 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: 2.07 (0.23), residues: 500 sheet: 0.41 (0.35), residues: 235 loop : -0.42 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 157 HIS 0.002 0.000 HIS A 632 PHE 0.007 0.001 PHE A 165 TYR 0.010 0.001 TYR B 373 ARG 0.002 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 482) hydrogen bonds : angle 4.01245 ( 1335) covalent geometry : bond 0.00226 (10309) covalent geometry : angle 0.42759 (13877) *********************** 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: 22 poor density : 108 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8723 (p90) cc_final: 0.8451 (p90) REVERT: A 374 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 465 GLU cc_start: 0.7952 (pp20) cc_final: 0.7538 (pp20) REVERT: A 553 MET cc_start: 0.7574 (tpp) cc_final: 0.7253 (tpp) REVERT: A 629 ASN cc_start: 0.9265 (t0) cc_final: 0.9041 (t0) REVERT: B 70 GLU cc_start: 0.8098 (tt0) cc_final: 0.7870 (tt0) REVERT: B 118 GLN cc_start: 0.9059 (pp30) cc_final: 0.8600 (pp30) REVERT: B 366 CYS cc_start: 0.8108 (t) cc_final: 0.7753 (m) REVERT: B 368 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: B 372 GLU cc_start: 0.8266 (tp30) cc_final: 0.7943 (tp30) REVERT: B 375 ASN cc_start: 0.8649 (p0) cc_final: 0.8398 (p0) REVERT: B 405 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8375 (ttm-80) REVERT: B 490 SER cc_start: 0.8476 (t) cc_final: 0.7819 (p) REVERT: B 515 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: B 544 PRO cc_start: 0.8880 (Cg_exo) cc_final: 0.8671 (Cg_endo) REVERT: B 553 MET cc_start: 0.6814 (tpp) cc_final: 0.6343 (tpp) REVERT: B 561 GLU cc_start: 0.8400 (pm20) cc_final: 0.8198 (pm20) REVERT: B 607 LYS cc_start: 0.8724 (tppt) cc_final: 0.8452 (mttm) REVERT: B 629 ASN cc_start: 0.9100 (t0) cc_final: 0.8827 (t0) REVERT: B 668 PHE cc_start: 0.8900 (m-80) cc_final: 0.8481 (m-80) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 0.2090 time to fit residues: 39.4336 Evaluate side-chains 120 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.099326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076778 restraints weight = 18364.693| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.91 r_work: 0.2804 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10309 Z= 0.152 Angle : 0.467 6.295 13877 Z= 0.245 Chirality : 0.040 0.159 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.256 56.668 1415 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.69 % Allowed : 12.91 % 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: 1.08 (0.25), residues: 1233 helix: 2.04 (0.23), residues: 499 sheet: 0.45 (0.36), residues: 225 loop : -0.47 (0.28), residues: 509 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 0.013 0.001 TYR B 134 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 482) hydrogen bonds : angle 4.08375 ( 1335) covalent geometry : bond 0.00360 (10309) covalent geometry : angle 0.46748 (13877) *********************** 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 121 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8679 (p90) cc_final: 0.8408 (p90) REVERT: A 343 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 374 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8558 (mp) REVERT: A 465 GLU cc_start: 0.8046 (pp20) cc_final: 0.7637 (pp20) REVERT: A 553 MET cc_start: 0.7452 (tpp) cc_final: 0.7131 (tpp) REVERT: A 629 ASN cc_start: 0.9268 (t0) cc_final: 0.9014 (t0) REVERT: B 70 GLU cc_start: 0.8112 (tt0) cc_final: 0.7875 (tt0) REVERT: B 118 GLN cc_start: 0.9084 (pp30) cc_final: 0.8624 (pp30) REVERT: B 366 CYS cc_start: 0.8124 (t) cc_final: 0.7795 (m) REVERT: B 368 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: B 490 SER cc_start: 0.8491 (t) cc_final: 0.7845 (p) REVERT: B 515 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: B 553 MET cc_start: 0.6834 (tpp) cc_final: 0.6356 (tpp) REVERT: B 607 LYS cc_start: 0.8726 (tppt) cc_final: 0.8451 (mttm) REVERT: B 629 ASN cc_start: 0.9132 (t0) cc_final: 0.8836 (t0) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.2172 time to fit residues: 37.0127 Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.098851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075847 restraints weight = 18450.278| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.01 r_work: 0.2785 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10309 Z= 0.170 Angle : 0.488 6.914 13877 Z= 0.256 Chirality : 0.040 0.159 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.312 54.817 1415 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.96 % Allowed : 13.54 % Favored : 84.51 % 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: 1.02 (0.25), residues: 1233 helix: 1.97 (0.23), residues: 505 sheet: 0.43 (0.36), residues: 225 loop : -0.51 (0.28), residues: 503 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 0.010 0.001 PHE B 15 TYR 0.015 0.002 TYR A 426 ARG 0.002 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 482) hydrogen bonds : angle 4.11931 ( 1335) covalent geometry : bond 0.00406 (10309) covalent geometry : angle 0.48786 (13877) *********************** 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: 22 poor density : 100 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8692 (p90) cc_final: 0.8417 (p90) REVERT: A 343 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 374 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 465 GLU cc_start: 0.8038 (pp20) cc_final: 0.7607 (pp20) REVERT: A 553 MET cc_start: 0.7397 (tpp) cc_final: 0.7060 (tpp) REVERT: A 606 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7994 (ptp) REVERT: A 629 ASN cc_start: 0.9274 (t0) cc_final: 0.8980 (t0) REVERT: B 70 GLU cc_start: 0.8160 (tt0) cc_final: 0.7888 (tt0) REVERT: B 118 GLN cc_start: 0.9096 (pp30) cc_final: 0.8629 (pp30) REVERT: B 366 CYS cc_start: 0.8111 (t) cc_final: 0.7765 (m) REVERT: B 368 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: B 372 GLU cc_start: 0.8173 (tp30) cc_final: 0.7829 (tp30) REVERT: B 490 SER cc_start: 0.8405 (t) cc_final: 0.7767 (p) REVERT: B 515 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: B 553 MET cc_start: 0.6924 (tpp) cc_final: 0.6437 (tpp) REVERT: B 607 LYS cc_start: 0.8642 (tppt) cc_final: 0.8253 (mmtp) REVERT: B 629 ASN cc_start: 0.9104 (t0) cc_final: 0.8765 (t0) outliers start: 22 outliers final: 13 residues processed: 113 average time/residue: 0.1928 time to fit residues: 32.4711 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 : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.098004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.075645 restraints weight = 18380.679| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.90 r_work: 0.2792 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10309 Z= 0.167 Angle : 0.485 7.378 13877 Z= 0.254 Chirality : 0.040 0.157 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.294 54.121 1415 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.87 % Allowed : 13.62 % Favored : 84.51 % 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: 1.03 (0.25), residues: 1233 helix: 1.99 (0.23), residues: 504 sheet: 0.43 (0.35), residues: 231 loop : -0.53 (0.28), residues: 498 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 0.009 0.001 PHE B 15 TYR 0.014 0.001 TYR A 426 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 482) hydrogen bonds : angle 4.11794 ( 1335) covalent geometry : bond 0.00397 (10309) covalent geometry : angle 0.48513 (13877) *********************** 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 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8684 (p90) cc_final: 0.8421 (p90) REVERT: A 343 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 374 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 465 GLU cc_start: 0.8073 (pp20) cc_final: 0.7648 (pp20) REVERT: A 553 MET cc_start: 0.7433 (tpp) cc_final: 0.7089 (tpp) REVERT: A 606 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8023 (ptp) REVERT: A 629 ASN cc_start: 0.9270 (t0) cc_final: 0.8989 (t0) REVERT: B 70 GLU cc_start: 0.8131 (tt0) cc_final: 0.7886 (tt0) REVERT: B 118 GLN cc_start: 0.9094 (pp30) cc_final: 0.8640 (pp30) REVERT: B 366 CYS cc_start: 0.8115 (t) cc_final: 0.7792 (m) REVERT: B 368 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: B 490 SER cc_start: 0.8453 (t) cc_final: 0.7815 (p) REVERT: B 515 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: B 553 MET cc_start: 0.6861 (tpp) cc_final: 0.6373 (tpp) REVERT: B 607 LYS cc_start: 0.8622 (tppt) cc_final: 0.8208 (mmtp) REVERT: B 629 ASN cc_start: 0.9111 (t0) cc_final: 0.8784 (t0) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.2114 time to fit residues: 34.9318 Evaluate side-chains 114 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.098652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077248 restraints weight = 18449.825| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.83 r_work: 0.2817 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10309 Z= 0.128 Angle : 0.463 7.994 13877 Z= 0.244 Chirality : 0.040 0.154 1545 Planarity : 0.003 0.037 1765 Dihedral : 5.141 53.656 1415 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 13.62 % Favored : 84.51 % 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 (0.23), residues: 506 sheet: 0.44 (0.35), residues: 230 loop : -0.46 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 157 HIS 0.002 0.000 HIS A 632 PHE 0.007 0.001 PHE B 15 TYR 0.011 0.001 TYR B 134 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 482) hydrogen bonds : angle 4.03351 ( 1335) covalent geometry : bond 0.00303 (10309) covalent geometry : angle 0.46307 (13877) *********************** 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: 21 poor density : 103 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8677 (p90) cc_final: 0.8426 (p90) REVERT: A 343 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8114 (tt) REVERT: A 374 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 465 GLU cc_start: 0.8021 (pp20) cc_final: 0.7602 (pp20) REVERT: A 553 MET cc_start: 0.7446 (tpp) cc_final: 0.7105 (tpp) REVERT: A 606 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7992 (ptp) REVERT: A 629 ASN cc_start: 0.9241 (t0) cc_final: 0.8979 (t0) REVERT: B 70 GLU cc_start: 0.8112 (tt0) cc_final: 0.7877 (tt0) REVERT: B 118 GLN cc_start: 0.9057 (pp30) cc_final: 0.8694 (pp30) REVERT: B 366 CYS cc_start: 0.8098 (t) cc_final: 0.7793 (m) REVERT: B 368 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: B 405 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8305 (ttm-80) REVERT: B 490 SER cc_start: 0.8436 (t) cc_final: 0.7566 (p) REVERT: B 494 VAL cc_start: 0.9201 (t) cc_final: 0.8794 (m) REVERT: B 515 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 553 MET cc_start: 0.6846 (tpp) cc_final: 0.6355 (tpp) REVERT: B 561 GLU cc_start: 0.8497 (pm20) cc_final: 0.7968 (pm20) REVERT: B 564 CYS cc_start: 0.8783 (m) cc_final: 0.8480 (m) REVERT: B 607 LYS cc_start: 0.8642 (tppt) cc_final: 0.8319 (mttm) REVERT: B 629 ASN cc_start: 0.9128 (t0) cc_final: 0.8838 (t0) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.2034 time to fit residues: 34.8339 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 188 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 7.9990 chunk 8 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.100266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078952 restraints weight = 18353.888| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.82 r_work: 0.2846 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10309 Z= 0.097 Angle : 0.448 8.501 13877 Z= 0.234 Chirality : 0.039 0.149 1545 Planarity : 0.003 0.038 1765 Dihedral : 4.988 54.172 1415 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.60 % Allowed : 14.07 % 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: 1.21 (0.25), residues: 1233 helix: 2.14 (0.24), residues: 505 sheet: 0.47 (0.35), residues: 241 loop : -0.43 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 157 HIS 0.002 0.000 HIS A 632 PHE 0.006 0.001 PHE B 15 TYR 0.009 0.001 TYR B 373 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 482) hydrogen bonds : angle 3.93128 ( 1335) covalent geometry : bond 0.00225 (10309) covalent geometry : angle 0.44824 (13877) ********************** 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 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8658 (p90) cc_final: 0.8426 (p90) REVERT: A 343 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8100 (tt) REVERT: A 465 GLU cc_start: 0.7871 (pp20) cc_final: 0.7444 (pp20) REVERT: A 553 MET cc_start: 0.7537 (tpp) cc_final: 0.7212 (tpp) REVERT: A 629 ASN cc_start: 0.9270 (t0) cc_final: 0.9053 (t0) REVERT: A 660 GLU cc_start: 0.9096 (tp30) cc_final: 0.8423 (mt-10) REVERT: A 663 LEU cc_start: 0.8778 (tp) cc_final: 0.8517 (mp) REVERT: B 70 GLU cc_start: 0.8100 (tt0) cc_final: 0.7871 (tt0) REVERT: B 118 GLN cc_start: 0.9067 (pp30) cc_final: 0.8614 (pp30) REVERT: B 366 CYS cc_start: 0.8002 (t) cc_final: 0.7665 (m) REVERT: B 368 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: B 405 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8283 (ttm-80) REVERT: B 490 SER cc_start: 0.8367 (t) cc_final: 0.7466 (p) REVERT: B 494 VAL cc_start: 0.9195 (t) cc_final: 0.8796 (m) REVERT: B 515 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: B 553 MET cc_start: 0.6740 (tpp) cc_final: 0.6269 (tpp) REVERT: B 561 GLU cc_start: 0.8490 (pm20) cc_final: 0.8021 (pm20) REVERT: B 607 LYS cc_start: 0.8647 (tppt) cc_final: 0.8326 (mttm) REVERT: B 629 ASN cc_start: 0.9120 (t0) cc_final: 0.8847 (t0) REVERT: B 668 PHE cc_start: 0.8805 (m-80) cc_final: 0.8372 (m-80) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.2064 time to fit residues: 34.8281 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 : 1.130 ------------------------------------------------------------------------------- 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 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 188 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.098554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.075824 restraints weight = 18335.312| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.94 r_work: 0.2790 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10309 Z= 0.189 Angle : 0.510 8.420 13877 Z= 0.265 Chirality : 0.041 0.162 1545 Planarity : 0.003 0.038 1765 Dihedral : 5.333 56.435 1415 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.78 % Allowed : 13.89 % 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: 1.04 (0.25), residues: 1233 helix: 1.98 (0.23), residues: 511 sheet: 0.38 (0.35), residues: 236 loop : -0.52 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.003 0.001 HIS B 632 PHE 0.010 0.001 PHE B 15 TYR 0.017 0.002 TYR A 426 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 482) hydrogen bonds : angle 4.12003 ( 1335) covalent geometry : bond 0.00450 (10309) covalent geometry : angle 0.51045 (13877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4408.73 seconds wall clock time: 77 minutes 30.81 seconds (4650.81 seconds total)