Starting phenix.real_space_refine on Fri Nov 15 06:26:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpy_29371/11_2024/8fpy_29371.cif" } resolution = 2.98 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.77, per 1000 atoms: 0.69 Number of scatterers: 8392 At special positions: 0 Unit cell: (120.54, 93.48, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1608 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 2.17 Conformation dependent library (CDL) restraints added in 931.9 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 20 sheets defined 41.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.641A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.593A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.859A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.554A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.109A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 715 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.502A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.502A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.668A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 444 removed outlier: 3.732A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.028A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.519A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 439 through 444 removed outlier: 3.537A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.902A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.548A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 removed outlier: 7.055A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.099A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.553A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1011 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: 2.28 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2630 1.35 - 1.47: 2036 1.47 - 1.60: 3728 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11327 1.97 - 3.95: 117 3.95 - 5.92: 41 5.92 - 7.90: 24 7.90 - 9.87: 11 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.62 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.52 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.07 -9.32 3.00e+00 1.11e-01 9.66e+00 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.02 -9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" O3 CYZ C1302 " pdb=" S2 CYZ C1302 " pdb=" O4 CYZ C1302 " ideal model delta sigma weight residual 118.35 109.33 9.02 3.00e+00 1.11e-01 9.03e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 4627 22.62 - 45.24: 493 45.24 - 67.86: 98 67.86 - 90.48: 20 90.48 - 113.10: 10 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 155.14 -62.14 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1183 0.087 - 0.173: 85 0.173 - 0.260: 0 0.260 - 0.346: 0 0.346 - 0.433: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C8 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" N2 CYZ B1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 772 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" CD GLU D 772 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D 772 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 772 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 736 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 737 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 737 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 737 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 438 " 0.006 2.00e-02 2.50e+03 8.60e-03 1.29e+00 pdb=" CG PHE C 438 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 438 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 438 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 438 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 438 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 438 " 0.000 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 90 2.64 - 3.20: 7218 3.20 - 3.77: 13092 3.77 - 4.33: 18567 4.33 - 4.90: 30217 Nonbonded interactions: 69184 Sorted by model distance: nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.069 3.040 nonbonded pdb=" NE2 GLN C 714 " pdb=" O TRP C 767 " model vdw 2.203 3.120 nonbonded pdb=" O PHE A 658 " pdb=" OG SER A 662 " model vdw 2.208 3.040 nonbonded pdb=" N ASP D 427 " pdb=" OD1 ASP D 427 " model vdw 2.216 3.120 nonbonded pdb=" O PHE C 658 " pdb=" OG SER C 662 " model vdw 2.274 3.040 ... (remaining 69179 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 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.820 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.015 0.244 8538 Z= 0.978 Angle : 0.696 9.871 11520 Z= 0.295 Chirality : 0.061 0.433 1284 Planarity : 0.003 0.030 1422 Dihedral : 19.339 113.100 3288 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.68 % Allowed : 31.99 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.27 (0.25), residues: 1044 helix: 0.86 (0.25), residues: 418 sheet: -0.38 (0.38), residues: 182 loop : -1.05 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.005 0.001 HIS B 412 PHE 0.020 0.001 PHE C 438 TYR 0.011 0.001 TYR B 673 ARG 0.007 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.941 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 1.5980 time to fit residues: 246.5174 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 625 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8538 Z= 0.219 Angle : 0.537 7.705 11520 Z= 0.265 Chirality : 0.044 0.162 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.452 91.303 1292 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.82 % Allowed : 26.62 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.26 (0.26), residues: 1044 helix: 0.88 (0.25), residues: 438 sheet: -0.39 (0.39), residues: 170 loop : -1.13 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.011 0.001 PHE B 495 TYR 0.018 0.002 TYR C 673 ARG 0.005 0.001 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.006 Fit side-chains REVERT: A 419 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: A 441 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7742 (tttm) REVERT: A 486 GLU cc_start: 0.7640 (tp30) cc_final: 0.7320 (mm-30) REVERT: C 684 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7047 (mtm180) REVERT: D 427 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6699 (p0) outliers start: 52 outliers final: 23 residues processed: 171 average time/residue: 1.5226 time to fit residues: 273.8084 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 742 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8538 Z= 0.217 Angle : 0.535 8.105 11520 Z= 0.264 Chirality : 0.044 0.216 1284 Planarity : 0.004 0.039 1422 Dihedral : 9.075 89.822 1278 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.38 % Allowed : 26.29 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.31 (0.25), residues: 1044 helix: 0.94 (0.25), residues: 434 sheet: -0.40 (0.37), residues: 180 loop : -1.26 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 460 HIS 0.005 0.001 HIS B 412 PHE 0.011 0.001 PHE B 495 TYR 0.015 0.001 TYR B 673 ARG 0.006 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.925 Fit side-chains REVERT: A 393 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5090 (pmtt) REVERT: A 419 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: A 486 GLU cc_start: 0.7587 (tp30) cc_final: 0.7237 (mm-30) REVERT: C 393 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4780 (pmmt) REVERT: C 751 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8295 (mt) REVERT: D 427 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: D 697 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7036 (mmmm) outliers start: 57 outliers final: 25 residues processed: 167 average time/residue: 1.5327 time to fit residues: 269.2163 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 27 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8538 Z= 0.162 Angle : 0.495 7.784 11520 Z= 0.244 Chirality : 0.043 0.192 1284 Planarity : 0.004 0.042 1422 Dihedral : 8.144 83.843 1277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.70 % Allowed : 28.08 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.16 (0.25), residues: 1044 helix: 1.03 (0.25), residues: 438 sheet: -0.09 (0.40), residues: 150 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.011 0.001 TYR D 673 ARG 0.008 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.962 Fit side-chains REVERT: A 393 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5124 (pmtt) REVERT: A 419 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6673 (tt0) REVERT: A 486 GLU cc_start: 0.7518 (tp30) cc_final: 0.7237 (mm-30) REVERT: A 708 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: C 708 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: C 719 ASP cc_start: 0.6356 (p0) cc_final: 0.5975 (p0) REVERT: D 427 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6958 (m-30) REVERT: D 628 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6735 (tpp80) outliers start: 42 outliers final: 18 residues processed: 164 average time/residue: 1.4934 time to fit residues: 257.8148 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8538 Z= 0.239 Angle : 0.550 8.494 11520 Z= 0.271 Chirality : 0.045 0.205 1284 Planarity : 0.004 0.043 1422 Dihedral : 7.834 84.282 1272 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.70 % Allowed : 28.08 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.30 (0.25), residues: 1044 helix: 0.91 (0.25), residues: 438 sheet: -0.44 (0.39), residues: 160 loop : -1.19 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.026 0.002 PHE A 438 TYR 0.016 0.002 TYR B 673 ARG 0.008 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.899 Fit side-chains REVERT: A 393 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5138 (pmtt) REVERT: A 419 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: A 486 GLU cc_start: 0.7565 (tp30) cc_final: 0.7242 (mm-30) REVERT: A 708 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7412 (mtp) REVERT: B 705 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: B 714 GLN cc_start: 0.7512 (tp40) cc_final: 0.6833 (tp40) REVERT: C 393 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.4926 (pmmt) REVERT: C 751 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8320 (mt) REVERT: D 427 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: D 628 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6758 (tpp80) outliers start: 51 outliers final: 26 residues processed: 162 average time/residue: 1.5184 time to fit residues: 258.3452 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 411 ASN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8538 Z= 0.300 Angle : 0.599 9.057 11520 Z= 0.297 Chirality : 0.047 0.217 1284 Planarity : 0.004 0.044 1422 Dihedral : 8.201 88.146 1272 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.38 % Allowed : 26.96 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.51 (0.25), residues: 1044 helix: 0.78 (0.25), residues: 434 sheet: -0.45 (0.40), residues: 148 loop : -1.37 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 PHE 0.013 0.002 PHE B 495 TYR 0.017 0.002 TYR B 673 ARG 0.008 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.958 Fit side-chains REVERT: A 393 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5074 (pmtt) REVERT: A 486 GLU cc_start: 0.7590 (tp30) cc_final: 0.7310 (mm-30) REVERT: A 684 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6926 (mtp180) REVERT: B 407 MET cc_start: 0.7960 (mtm) cc_final: 0.7691 (mtm) REVERT: C 393 LYS cc_start: 0.5365 (OUTLIER) cc_final: 0.4909 (pmmt) REVERT: C 751 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (mt) REVERT: D 628 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6758 (tpp80) outliers start: 57 outliers final: 35 residues processed: 162 average time/residue: 1.5135 time to fit residues: 258.6719 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8538 Z= 0.179 Angle : 0.520 7.840 11520 Z= 0.260 Chirality : 0.043 0.187 1284 Planarity : 0.004 0.046 1422 Dihedral : 7.464 83.777 1270 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.26 % Allowed : 28.30 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1044 helix: 0.93 (0.26), residues: 438 sheet: -0.35 (0.37), residues: 158 loop : -1.36 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.025 0.002 PHE A 438 TYR 0.012 0.001 TYR D 673 ARG 0.010 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.981 Fit side-chains REVERT: A 393 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5030 (pmtt) REVERT: A 419 GLU cc_start: 0.7171 (tp30) cc_final: 0.6917 (tt0) REVERT: A 486 GLU cc_start: 0.7484 (tp30) cc_final: 0.7169 (mm-30) REVERT: A 684 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6875 (mtp180) REVERT: B 714 GLN cc_start: 0.7532 (tp40) cc_final: 0.6916 (tp40) REVERT: C 393 LYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4693 (pmmt) REVERT: C 708 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: C 751 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8298 (mt) REVERT: D 628 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6754 (tpp80) outliers start: 47 outliers final: 26 residues processed: 158 average time/residue: 1.5164 time to fit residues: 252.7286 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8538 Z= 0.174 Angle : 0.514 7.877 11520 Z= 0.257 Chirality : 0.043 0.173 1284 Planarity : 0.004 0.047 1422 Dihedral : 7.040 74.683 1270 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.81 % Allowed : 28.64 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.34 (0.25), residues: 1044 helix: 0.96 (0.26), residues: 438 sheet: -0.35 (0.40), residues: 132 loop : -1.33 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.012 0.001 TYR D 673 ARG 0.012 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.957 Fit side-chains REVERT: A 419 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: A 486 GLU cc_start: 0.7473 (tp30) cc_final: 0.7198 (mm-30) REVERT: A 684 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: A 703 LEU cc_start: 0.8032 (mt) cc_final: 0.7792 (mt) REVERT: A 708 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (mtp) REVERT: B 714 GLN cc_start: 0.7552 (tp40) cc_final: 0.6935 (tp40) REVERT: C 393 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4677 (pmmt) REVERT: C 708 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7451 (mtp) REVERT: D 454 ASP cc_start: 0.5333 (t0) cc_final: 0.5124 (m-30) REVERT: D 628 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6676 (tpp80) outliers start: 43 outliers final: 28 residues processed: 157 average time/residue: 1.5238 time to fit residues: 251.5711 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.179 Angle : 0.525 7.829 11520 Z= 0.263 Chirality : 0.043 0.225 1284 Planarity : 0.004 0.053 1422 Dihedral : 6.402 56.232 1270 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.59 % Allowed : 28.86 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.33 (0.25), residues: 1044 helix: 0.94 (0.26), residues: 438 sheet: -0.25 (0.40), residues: 132 loop : -1.32 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.027 0.001 PHE A 438 TYR 0.012 0.001 TYR D 673 ARG 0.012 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.957 Fit side-chains REVERT: A 419 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: A 473 ASP cc_start: 0.7823 (m-30) cc_final: 0.7520 (m-30) REVERT: A 486 GLU cc_start: 0.7494 (tp30) cc_final: 0.7224 (mm-30) REVERT: A 684 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6905 (mtp180) REVERT: A 703 LEU cc_start: 0.8042 (mt) cc_final: 0.7809 (mt) REVERT: A 708 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7368 (mtp) REVERT: B 674 MET cc_start: 0.8368 (mtp) cc_final: 0.7993 (mtt) REVERT: B 714 GLN cc_start: 0.7472 (tp40) cc_final: 0.6839 (tp40) REVERT: C 393 LYS cc_start: 0.5081 (OUTLIER) cc_final: 0.4595 (pmmt) REVERT: C 708 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7434 (mtp) REVERT: C 715 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6029 (ttm110) REVERT: C 719 ASP cc_start: 0.6456 (p0) cc_final: 0.6034 (p0) REVERT: D 454 ASP cc_start: 0.5351 (t0) cc_final: 0.5145 (m-30) REVERT: D 628 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6678 (tpp80) outliers start: 41 outliers final: 30 residues processed: 152 average time/residue: 1.4759 time to fit residues: 236.4258 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN D 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8538 Z= 0.200 Angle : 0.541 7.855 11520 Z= 0.271 Chirality : 0.044 0.192 1284 Planarity : 0.004 0.055 1422 Dihedral : 6.242 55.272 1270 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.59 % Allowed : 29.08 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.29 (0.25), residues: 1044 helix: 0.94 (0.26), residues: 436 sheet: -0.19 (0.38), residues: 158 loop : -1.32 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.022 0.001 TYR C 673 ARG 0.013 0.001 ARG D 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.002 Fit side-chains REVERT: A 419 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: A 473 ASP cc_start: 0.7861 (m-30) cc_final: 0.7530 (m-30) REVERT: A 486 GLU cc_start: 0.7511 (tp30) cc_final: 0.7237 (mm-30) REVERT: A 684 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6859 (mtp180) REVERT: A 708 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7346 (mtp) REVERT: B 674 MET cc_start: 0.8400 (mtp) cc_final: 0.8059 (mtt) REVERT: B 714 GLN cc_start: 0.7473 (tp40) cc_final: 0.6841 (tp40) REVERT: C 393 LYS cc_start: 0.5099 (OUTLIER) cc_final: 0.4638 (pmmt) REVERT: C 708 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7410 (mtp) REVERT: C 715 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6026 (ttm110) REVERT: C 719 ASP cc_start: 0.6481 (p0) cc_final: 0.6058 (p0) REVERT: D 454 ASP cc_start: 0.5361 (t0) cc_final: 0.5123 (m-30) REVERT: D 628 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6668 (tpp80) outliers start: 41 outliers final: 30 residues processed: 148 average time/residue: 1.4731 time to fit residues: 229.6480 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN D 411 ASN D 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128284 restraints weight = 10663.250| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.07 r_work: 0.3395 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8538 Z= 0.195 Angle : 0.537 7.821 11520 Z= 0.270 Chirality : 0.044 0.172 1284 Planarity : 0.004 0.055 1422 Dihedral : 6.115 54.997 1269 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.59 % Allowed : 29.08 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.26 (0.25), residues: 1044 helix: 0.96 (0.26), residues: 436 sheet: -0.14 (0.38), residues: 158 loop : -1.30 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.012 0.001 TYR D 673 ARG 0.013 0.001 ARG D 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4064.26 seconds wall clock time: 73 minutes 23.67 seconds (4403.67 seconds total)