Starting phenix.real_space_refine on Fri Aug 22 22:54:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_29372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_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/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_29372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_29372.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_29372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpz_29372/08_2025/8fpz_29372.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.84, per 1000 atoms: 0.22 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: 0.54 Conformation dependent library (CDL) restraints added in 267.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.32 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: 1.16 Time building geometry restraints manager: 0.69 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 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- 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 8542 Z= 0.726 Angle : 0.727 9.528 11528 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG C 661 TYR 0.010 0.001 TYR B 405 PHE 0.020 0.001 PHE A 438 TRP 0.009 0.001 TRP C 671 HIS 0.002 0.000 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.01458 ( 8538) covalent geometry : angle 0.72706 (11520) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.57748 ( 8) hydrogen bonds : bond 0.16472 ( 328) hydrogen bonds : angle 6.46707 ( 972) *********************** 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 : 0.297 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: 0.6422 (tptp) 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: 0.7163 (mm-30) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.1104 time to fit residues: 17.6855 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 : 0.473 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.166115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142611 restraints weight = 11028.098| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.02 r_work: 0.3637 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.125 Angle : 0.502 6.763 11528 Z= 0.252 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.550 96.307 1267 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.45 % Allowed : 17.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 1044 helix: 0.79 (0.25), residues: 436 sheet: -1.04 (0.38), residues: 158 loop : -1.12 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 661 TYR 0.012 0.001 TYR B 405 PHE 0.017 0.002 PHE A 438 TRP 0.011 0.001 TRP C 671 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8538) covalent geometry : angle 0.50219 (11520) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.59038 ( 8) hydrogen bonds : bond 0.03092 ( 328) hydrogen bonds : angle 4.62906 ( 972) *********************** 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: 13 poor density : 135 time to evaluate : 0.262 Fit side-chains REVERT: A 637 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6985 (tt0) REVERT: C 634 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7373 (mm-30) outliers start: 13 outliers final: 6 residues processed: 147 average time/residue: 0.0924 time to fit residues: 17.8771 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 : 0.198 ------------------------------------------------------------------------------- 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 81 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 40 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142326 restraints weight = 10933.110| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.99 r_work: 0.3633 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8542 Z= 0.122 Angle : 0.493 7.418 11528 Z= 0.247 Chirality : 0.044 0.138 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.355 93.796 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.46 % Allowed : 16.33 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.26), residues: 1044 helix: 0.90 (0.26), residues: 432 sheet: -1.07 (0.38), residues: 158 loop : -1.15 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 661 TYR 0.011 0.001 TYR B 405 PHE 0.011 0.001 PHE D 659 TRP 0.008 0.001 TRP C 671 HIS 0.001 0.000 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8538) covalent geometry : angle 0.49329 (11520) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.55057 ( 8) hydrogen bonds : bond 0.02923 ( 328) hydrogen bonds : angle 4.40653 ( 972) *********************** 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.236 Fit side-chains REVERT: A 458 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6959 (mmtm) REVERT: A 637 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7003 (tt0) REVERT: B 414 MET cc_start: 0.6168 (pmm) cc_final: 0.5720 (mpp) REVERT: C 634 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7279 (mm-30) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 0.0926 time to fit residues: 18.6219 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.164855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141378 restraints weight = 11220.089| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.01 r_work: 0.3622 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8542 Z= 0.125 Angle : 0.498 7.205 11528 Z= 0.249 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.203 93.141 1266 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.80 % Allowed : 16.33 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.26), residues: 1044 helix: 0.93 (0.25), residues: 430 sheet: -1.04 (0.38), residues: 158 loop : -1.12 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 661 TYR 0.011 0.001 TYR B 405 PHE 0.018 0.002 PHE A 438 TRP 0.008 0.001 TRP C 671 HIS 0.001 0.000 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8538) covalent geometry : angle 0.49808 (11520) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.54572 ( 8) hydrogen bonds : bond 0.02820 ( 328) hydrogen bonds : angle 4.33286 ( 972) *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.200 Fit side-chains REVERT: B 414 MET cc_start: 0.6234 (pmm) cc_final: 0.5806 (mpp) REVERT: D 435 HIS cc_start: 0.6034 (m90) cc_final: 0.5583 (m90) REVERT: D 714 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7495 (mm-40) outliers start: 25 outliers final: 22 residues processed: 156 average time/residue: 0.0844 time to fit residues: 17.4378 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL 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 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 41 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137017 restraints weight = 11166.023| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.00 r_work: 0.3570 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8542 Z= 0.216 Angle : 0.581 8.825 11528 Z= 0.293 Chirality : 0.047 0.199 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.977 101.870 1266 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.47 % Allowed : 17.67 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.25), residues: 1044 helix: 0.58 (0.25), residues: 430 sheet: -1.15 (0.40), residues: 144 loop : -1.16 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 661 TYR 0.016 0.002 TYR B 405 PHE 0.015 0.002 PHE D 659 TRP 0.008 0.001 TRP C 671 HIS 0.002 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 8538) covalent geometry : angle 0.58048 (11520) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.78525 ( 8) hydrogen bonds : bond 0.03603 ( 328) hydrogen bonds : angle 4.49014 ( 972) *********************** 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: 31 poor density : 126 time to evaluate : 0.312 Fit side-chains REVERT: A 466 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: B 414 MET cc_start: 0.6133 (pmm) cc_final: 0.5685 (mpp) REVERT: C 760 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7728 (t0) outliers start: 31 outliers final: 22 residues processed: 150 average time/residue: 0.0921 time to fit residues: 18.1566 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138198 restraints weight = 11108.881| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.00 r_work: 0.3578 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8542 Z= 0.169 Angle : 0.545 8.999 11528 Z= 0.273 Chirality : 0.045 0.170 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.566 98.152 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.36 % Allowed : 18.34 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.25), residues: 1044 helix: 0.65 (0.25), residues: 430 sheet: -1.20 (0.41), residues: 140 loop : -1.13 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 661 TYR 0.012 0.002 TYR B 405 PHE 0.017 0.002 PHE A 438 TRP 0.009 0.001 TRP C 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8538) covalent geometry : angle 0.54444 (11520) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.69014 ( 8) hydrogen bonds : bond 0.03213 ( 328) hydrogen bonds : angle 4.39038 ( 972) *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.304 Fit side-chains REVERT: A 466 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: B 414 MET cc_start: 0.6193 (pmm) cc_final: 0.5788 (mpp) REVERT: D 634 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6692 (tp30) outliers start: 30 outliers final: 21 residues processed: 150 average time/residue: 0.0957 time to fit residues: 18.5762 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 443 THR Chi-restraints excluded: chain B residue 474 ILE 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 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 693 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.165533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142309 restraints weight = 11107.475| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.04 r_work: 0.3619 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8542 Z= 0.102 Angle : 0.489 7.899 11528 Z= 0.245 Chirality : 0.043 0.201 1284 Planarity : 0.004 0.037 1422 Dihedral : 9.541 92.233 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.24 % Allowed : 19.69 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1044 helix: 0.99 (0.26), residues: 430 sheet: -1.10 (0.38), residues: 154 loop : -1.09 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 661 TYR 0.009 0.001 TYR C 673 PHE 0.019 0.001 PHE A 438 TRP 0.008 0.001 TRP C 671 HIS 0.001 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8538) covalent geometry : angle 0.48923 (11520) SS BOND : bond 0.00451 ( 4) SS BOND : angle 0.77409 ( 8) hydrogen bonds : bond 0.02568 ( 328) hydrogen bonds : angle 4.24213 ( 972) *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.234 Fit side-chains REVERT: B 414 MET cc_start: 0.6156 (pmm) cc_final: 0.5222 (mpp) REVERT: B 629 MET cc_start: 0.8313 (tpp) cc_final: 0.8021 (tpp) REVERT: B 642 GLN cc_start: 0.8023 (pp30) cc_final: 0.7608 (pp30) REVERT: D 435 HIS cc_start: 0.6062 (m90) cc_final: 0.5684 (m90) REVERT: D 511 LYS cc_start: 0.8002 (mttt) cc_final: 0.7407 (mtmm) REVERT: D 634 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6631 (tp30) REVERT: D 772 GLU cc_start: 0.5704 (tm-30) cc_final: 0.5466 (mm-30) outliers start: 20 outliers final: 17 residues processed: 150 average time/residue: 0.0904 time to fit residues: 17.7026 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 736 THR 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 48 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141652 restraints weight = 10974.297| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.99 r_work: 0.3629 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.111 Angle : 0.499 7.908 11528 Z= 0.250 Chirality : 0.043 0.138 1284 Planarity : 0.004 0.036 1422 Dihedral : 9.139 92.387 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.13 % Allowed : 19.91 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1044 helix: 1.07 (0.26), residues: 430 sheet: -0.97 (0.38), residues: 158 loop : -1.10 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.008 0.001 TYR B 405 PHE 0.019 0.001 PHE A 438 TRP 0.008 0.001 TRP C 671 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8538) covalent geometry : angle 0.49861 (11520) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.51894 ( 8) hydrogen bonds : bond 0.02633 ( 328) hydrogen bonds : angle 4.20122 ( 972) *********************** 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 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.310 Fit side-chains REVERT: B 414 MET cc_start: 0.6153 (pmm) cc_final: 0.5206 (mpp) REVERT: B 629 MET cc_start: 0.8341 (tpp) cc_final: 0.8059 (tpp) REVERT: D 435 HIS cc_start: 0.6019 (m90) cc_final: 0.5637 (m90) REVERT: D 634 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6646 (tp30) REVERT: D 772 GLU cc_start: 0.5919 (tm-30) cc_final: 0.5493 (mm-30) outliers start: 19 outliers final: 18 residues processed: 144 average time/residue: 0.0852 time to fit residues: 16.3303 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 398 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.162176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138751 restraints weight = 11086.102| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.99 r_work: 0.3588 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8542 Z= 0.163 Angle : 0.543 8.947 11528 Z= 0.273 Chirality : 0.045 0.164 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.308 97.341 1266 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.46 % Allowed : 19.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.26), residues: 1044 helix: 0.89 (0.26), residues: 430 sheet: -1.11 (0.38), residues: 158 loop : -1.12 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 661 TYR 0.012 0.001 TYR B 405 PHE 0.018 0.002 PHE C 438 TRP 0.007 0.001 TRP C 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8538) covalent geometry : angle 0.54265 (11520) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.80447 ( 8) hydrogen bonds : bond 0.03148 ( 328) hydrogen bonds : angle 4.29322 ( 972) *********************** 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 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.225 Fit side-chains REVERT: B 414 MET cc_start: 0.6165 (pmm) cc_final: 0.5754 (mpp) REVERT: B 629 MET cc_start: 0.8378 (tpp) cc_final: 0.8109 (tpp) REVERT: C 408 MET cc_start: 0.7888 (mmm) cc_final: 0.7657 (mmm) REVERT: D 435 HIS cc_start: 0.6062 (m90) cc_final: 0.5657 (m90) REVERT: D 634 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6756 (tp30) REVERT: D 772 GLU cc_start: 0.6029 (tm-30) cc_final: 0.5442 (mm-30) outliers start: 22 outliers final: 18 residues processed: 140 average time/residue: 0.0879 time to fit residues: 16.1612 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 736 THR 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 41 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.163610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140438 restraints weight = 11104.314| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.00 r_work: 0.3614 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8542 Z= 0.130 Angle : 0.513 8.413 11528 Z= 0.258 Chirality : 0.044 0.208 1284 Planarity : 0.004 0.039 1422 Dihedral : 8.716 94.594 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 20.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.26), residues: 1044 helix: 0.97 (0.26), residues: 430 sheet: -1.07 (0.38), residues: 158 loop : -1.12 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 661 TYR 0.009 0.001 TYR D 421 PHE 0.020 0.002 PHE A 438 TRP 0.008 0.001 TRP C 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8538) covalent geometry : angle 0.51282 (11520) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.63369 ( 8) hydrogen bonds : bond 0.02802 ( 328) hydrogen bonds : angle 4.24469 ( 972) ********************** 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 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.230 Fit side-chains REVERT: B 414 MET cc_start: 0.6215 (pmm) cc_final: 0.5298 (mpp) REVERT: B 629 MET cc_start: 0.8346 (tpp) cc_final: 0.8066 (tpp) REVERT: D 435 HIS cc_start: 0.5982 (m90) cc_final: 0.5601 (m90) REVERT: D 634 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6791 (tp30) REVERT: D 772 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5482 (mm-30) outliers start: 17 outliers final: 17 residues processed: 139 average time/residue: 0.0800 time to fit residues: 14.9486 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 736 THR 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 8 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.165546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142643 restraints weight = 11002.440| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.99 r_work: 0.3635 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8542 Z= 0.103 Angle : 0.496 9.296 11528 Z= 0.250 Chirality : 0.043 0.140 1284 Planarity : 0.004 0.037 1422 Dihedral : 8.274 91.756 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.90 % Allowed : 20.36 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.26), residues: 1044 helix: 1.11 (0.26), residues: 430 sheet: -1.02 (0.37), residues: 166 loop : -1.14 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 661 TYR 0.008 0.001 TYR B 673 PHE 0.020 0.001 PHE A 438 TRP 0.007 0.001 TRP D 671 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8538) covalent geometry : angle 0.49640 (11520) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.46530 ( 8) hydrogen bonds : bond 0.02535 ( 328) hydrogen bonds : angle 4.19029 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.88 seconds wall clock time: 32 minutes 15.40 seconds (1935.40 seconds total)