Starting phenix.real_space_refine on Fri Nov 15 06:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpz_29372/11_2024/8fpz_29372.cif" } resolution = 3.01 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= 0.003 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 27 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.27, per 1000 atoms: 0.75 Number of scatterers: 8392 At special positions: 0 Unit cell: (120.54, 95.94, 83.64, 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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 17 sheets defined 41.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.711A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.607A pdb=" N GLY A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.512A 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: 4.393A 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: 3.936A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 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 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.781A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) 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 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.727A 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 655 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 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 423 through 436 removed outlier: 4.195A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) 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 removed outlier: 3.694A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.543A pdb=" N ARG D 715 " --> pdb=" O TYR D 711 " (cutoff:3.500A) 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: 6.485A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 removed outlier: 4.097A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.671A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.671A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (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 646 through 648 removed outlier: 6.529A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.565A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.396A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 490 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.396A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.530A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 439 through 444 removed outlier: 3.580A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AB6, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.810A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.466A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 972 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: 2.44 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2044 1.48 - 1.60: 3720 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " 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 C1302 " pdb=" C4 CYZ C1302 " 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 D1302 " pdb=" C4 CYZ D1302 " 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 B1302 " pdb=" C4 CYZ B1302 " 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 A1302 " pdb=" C6 CYZ A1302 " 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 - 1.91: 11286 1.91 - 3.81: 154 3.81 - 5.72: 36 5.72 - 7.62: 23 7.62 - 9.53: 21 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.28 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.19 -9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.14 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.10 -9.35 3.00e+00 1.11e-01 9.72e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.31 9.04 3.00e+00 1.11e-01 9.08e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 4761 22.86 - 45.73: 411 45.73 - 68.59: 48 68.59 - 91.45: 16 91.45 - 114.32: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 93.00 171.79 -78.79 1 1.00e+01 1.00e-02 7.73e+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 93.00 165.79 -72.79 1 1.00e+01 1.00e-02 6.76e+01 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 93.00 159.30 -66.30 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1176 0.085 - 0.170: 91 0.170 - 0.255: 1 0.255 - 0.340: 0 0.340 - 0.425: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.52e+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 4.52e+00 chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 438 " 0.006 2.00e-02 2.50e+03 8.83e-03 1.36e+00 pdb=" CG PHE A 438 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 438 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 438 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 438 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 438 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 438 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 744 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO A 745 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO C 737 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.015 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1058 2.75 - 3.29: 7950 3.29 - 3.83: 14355 3.83 - 4.36: 17048 4.36 - 4.90: 29356 Nonbonded interactions: 69767 Sorted by model distance: nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU B 705 " pdb=" O HOH B1401 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLU B 402 " pdb=" OH TYR B 450 " model vdw 2.280 3.040 ... (remaining 69762 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: 3.870 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 23.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 0.243 8538 Z= 0.893 Angle : 0.727 9.528 11520 Z= 0.318 Chirality : 0.062 0.425 1284 Planarity : 0.003 0.036 1422 Dihedral : 17.385 114.317 3288 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.11 % Allowed : 17.34 % Favored : 82.55 % 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: -0.61 (0.25), residues: 1044 helix: 0.75 (0.25), residues: 428 sheet: -1.16 (0.36), residues: 170 loop : -1.17 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 671 HIS 0.002 0.000 HIS A 412 PHE 0.020 0.001 PHE A 438 TYR 0.010 0.001 TYR B 405 ARG 0.009 0.001 ARG C 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 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.985 Fit side-chains REVERT: A 637 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6813 (tt0) REVERT: A 699 LYS cc_start: 0.6696 (tttp) cc_final: 0.6392 (ttmm) REVERT: B 414 MET cc_start: 0.6072 (pmm) cc_final: 0.5625 (mpp) REVERT: C 634 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7162 (mm-30) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.2821 time to fit residues: 44.7271 Evaluate side-chains 119 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 720 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN D 435 HIS D 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8538 Z= 0.182 Angle : 0.497 6.453 11520 Z= 0.249 Chirality : 0.044 0.157 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.372 94.875 1267 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.34 % Allowed : 17.11 % Favored : 81.54 % 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: -0.47 (0.26), residues: 1044 helix: 0.83 (0.26), residues: 436 sheet: -1.02 (0.38), residues: 158 loop : -1.13 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 671 HIS 0.001 0.001 HIS C 435 PHE 0.016 0.002 PHE A 438 TYR 0.012 0.001 TYR B 405 ARG 0.004 0.000 ARG A 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 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.019 Fit side-chains REVERT: C 634 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7066 (mm-30) outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.2592 time to fit residues: 49.9355 Evaluate side-chains 130 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 0.0070 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 0.0040 chunk 77 optimal weight: 2.9990 overall best weight: 0.8212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8538 Z= 0.168 Angle : 0.483 6.704 11520 Z= 0.241 Chirality : 0.043 0.135 1284 Planarity : 0.003 0.037 1422 Dihedral : 9.987 90.418 1266 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 15.66 % Favored : 81.77 % 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: -0.44 (0.26), residues: 1044 helix: 0.92 (0.26), residues: 434 sheet: -1.02 (0.38), residues: 158 loop : -1.17 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.001 0.000 HIS B 412 PHE 0.010 0.001 PHE D 659 TYR 0.010 0.001 TYR C 673 ARG 0.004 0.000 ARG A 661 *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.956 Fit side-chains REVERT: B 414 MET cc_start: 0.6260 (pmm) cc_final: 0.5734 (mpp) REVERT: C 634 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7064 (mm-30) outliers start: 23 outliers final: 14 residues processed: 155 average time/residue: 0.2600 time to fit residues: 52.2686 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1279 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 : 0.492 7.169 11520 Z= 0.245 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.037 1422 Dihedral : 9.583 91.068 1266 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 16.44 % Favored : 80.98 % 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: -0.39 (0.26), residues: 1044 helix: 0.97 (0.26), residues: 432 sheet: -0.98 (0.38), residues: 158 loop : -1.15 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.001 0.000 HIS B 412 PHE 0.018 0.001 PHE A 438 TYR 0.010 0.001 TYR B 405 ARG 0.004 0.000 ARG A 661 *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.012 Fit side-chains REVERT: B 414 MET cc_start: 0.6272 (pmm) cc_final: 0.5806 (mpp) REVERT: C 634 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 435 HIS cc_start: 0.5954 (m90) cc_final: 0.5518 (m90) REVERT: D 714 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7246 (mm-40) outliers start: 23 outliers final: 20 residues processed: 155 average time/residue: 0.2555 time to fit residues: 51.7479 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0870 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 ASN C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8538 Z= 0.144 Angle : 0.474 7.080 11520 Z= 0.235 Chirality : 0.043 0.190 1284 Planarity : 0.003 0.036 1422 Dihedral : 8.613 88.407 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.68 % Allowed : 17.11 % Favored : 80.20 % 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 (0.26), residues: 1044 helix: 1.08 (0.26), residues: 434 sheet: -0.95 (0.37), residues: 166 loop : -1.10 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE D 659 TYR 0.009 0.001 TYR C 673 ARG 0.005 0.000 ARG C 661 *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.926 Fit side-chains REVERT: B 414 MET cc_start: 0.6336 (pmm) cc_final: 0.5876 (mpp) outliers start: 24 outliers final: 20 residues processed: 154 average time/residue: 0.2545 time to fit residues: 51.6941 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8538 Z= 0.418 Angle : 0.639 9.416 11520 Z= 0.324 Chirality : 0.050 0.238 1284 Planarity : 0.005 0.041 1422 Dihedral : 9.911 103.044 1266 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.36 % Allowed : 17.67 % Favored : 78.97 % 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: -0.78 (0.25), residues: 1044 helix: 0.46 (0.25), residues: 430 sheet: -1.37 (0.38), residues: 164 loop : -1.05 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 460 HIS 0.003 0.001 HIS C 435 PHE 0.018 0.002 PHE D 659 TYR 0.017 0.002 TYR B 405 ARG 0.006 0.001 ARG C 661 *********************** 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 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.960 Fit side-chains REVERT: A 466 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: B 414 MET cc_start: 0.6189 (pmm) cc_final: 0.5736 (mpp) REVERT: B 498 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8626 (pt) REVERT: C 760 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7629 (t0) REVERT: D 411 ASN cc_start: 0.7387 (p0) cc_final: 0.7111 (p0) REVERT: D 435 HIS cc_start: 0.6050 (m90) cc_final: 0.5620 (m90) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.2628 time to fit residues: 50.5992 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1745 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 : 0.500 8.079 11520 Z= 0.252 Chirality : 0.044 0.198 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.677 92.991 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.68 % Allowed : 18.57 % Favored : 78.75 % 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: -0.41 (0.26), residues: 1044 helix: 0.89 (0.26), residues: 430 sheet: -1.07 (0.41), residues: 140 loop : -1.06 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 671 HIS 0.001 0.000 HIS A 412 PHE 0.019 0.001 PHE A 438 TYR 0.009 0.001 TYR B 673 ARG 0.006 0.000 ARG A 661 *********************** 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 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.907 Fit side-chains REVERT: B 414 MET cc_start: 0.6289 (pmm) cc_final: 0.5810 (mpp) REVERT: D 435 HIS cc_start: 0.5942 (m90) cc_final: 0.5497 (m90) REVERT: D 772 GLU cc_start: 0.5965 (tm-30) cc_final: 0.5758 (mm-30) outliers start: 24 outliers final: 17 residues processed: 153 average time/residue: 0.2669 time to fit residues: 53.3865 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 0.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.147 Angle : 0.482 7.269 11520 Z= 0.244 Chirality : 0.043 0.138 1284 Planarity : 0.004 0.035 1422 Dihedral : 7.994 88.943 1266 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.68 % Allowed : 19.91 % Favored : 78.41 % 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: -0.24 (0.26), residues: 1044 helix: 1.12 (0.26), residues: 430 sheet: -0.99 (0.37), residues: 166 loop : -1.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 671 HIS 0.002 0.001 HIS D 412 PHE 0.019 0.001 PHE C 438 TYR 0.008 0.001 TYR B 673 ARG 0.007 0.001 ARG C 661 *********************** 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 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.044 Fit side-chains REVERT: B 414 MET cc_start: 0.6275 (pmm) cc_final: 0.5276 (mpp) REVERT: D 435 HIS cc_start: 0.5901 (m90) cc_final: 0.5476 (m90) REVERT: D 511 LYS cc_start: 0.7851 (mttt) cc_final: 0.7366 (mtmm) REVERT: D 772 GLU cc_start: 0.6076 (tm-30) cc_final: 0.5783 (mm-30) outliers start: 15 outliers final: 15 residues processed: 143 average time/residue: 0.2536 time to fit residues: 48.0721 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8538 Z= 0.277 Angle : 0.550 8.662 11520 Z= 0.279 Chirality : 0.046 0.177 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.788 97.346 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.79 % Allowed : 20.58 % Favored : 77.63 % 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: -0.47 (0.26), residues: 1044 helix: 0.83 (0.25), residues: 430 sheet: -1.08 (0.38), residues: 158 loop : -1.08 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.002 0.001 HIS C 412 PHE 0.018 0.002 PHE A 438 TYR 0.014 0.002 TYR B 405 ARG 0.007 0.001 ARG C 661 *********************** 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 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.000 Fit side-chains REVERT: B 414 MET cc_start: 0.6220 (pmm) cc_final: 0.5745 (mpp) REVERT: D 435 HIS cc_start: 0.5968 (m90) cc_final: 0.5540 (m90) REVERT: D 634 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6450 (tp30) REVERT: D 772 GLU cc_start: 0.6190 (tm-30) cc_final: 0.5823 (mm-30) outliers start: 16 outliers final: 15 residues processed: 135 average time/residue: 0.2590 time to fit residues: 46.2402 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8538 Z= 0.176 Angle : 0.505 7.908 11520 Z= 0.255 Chirality : 0.044 0.145 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.353 92.454 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.79 % Allowed : 20.58 % Favored : 77.63 % 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 (0.26), residues: 1044 helix: 1.01 (0.26), residues: 430 sheet: -1.12 (0.38), residues: 162 loop : -1.07 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.002 0.001 HIS C 412 PHE 0.020 0.001 PHE A 438 TYR 0.008 0.001 TYR D 421 ARG 0.008 0.001 ARG C 661 ********************** 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 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.002 Fit side-chains REVERT: B 414 MET cc_start: 0.6235 (pmm) cc_final: 0.5232 (mpp) REVERT: C 408 MET cc_start: 0.7765 (mmm) cc_final: 0.7550 (mmm) REVERT: D 435 HIS cc_start: 0.5901 (m90) cc_final: 0.5475 (m90) REVERT: D 634 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6458 (tp30) REVERT: D 772 GLU cc_start: 0.6082 (tm-30) cc_final: 0.5692 (mm-30) outliers start: 16 outliers final: 15 residues processed: 138 average time/residue: 0.2457 time to fit residues: 45.1299 Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.166649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143991 restraints weight = 10970.994| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.98 r_work: 0.3651 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.148 Angle : 0.485 7.090 11520 Z= 0.244 Chirality : 0.043 0.139 1284 Planarity : 0.004 0.038 1422 Dihedral : 7.761 87.048 1266 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 20.58 % Favored : 77.63 % 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: -0.24 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 432 sheet: -0.93 (0.37), residues: 166 loop : -1.11 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.001 0.000 HIS C 412 PHE 0.021 0.001 PHE C 438 TYR 0.007 0.001 TYR B 673 ARG 0.008 0.001 ARG C 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.40 seconds wall clock time: 40 minutes 8.46 seconds (2408.46 seconds total)