Starting phenix.real_space_refine on Sat Jun 7 03:31:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpz_29372/06_2025/8fpz_29372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpz_29372/06_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_29372/06_2025/8fpz_29372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpz_29372/06_2025/8fpz_29372.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpz_29372/06_2025/8fpz_29372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpz_29372/06_2025/8fpz_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-5710/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: 6.76, per 1000 atoms: 0.81 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: 2.18 Conformation dependent library (CDL) restraints added in 1.6 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: 1.19 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: 2.48 Time building geometry restraints manager: 2.57 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.700 Find NCS groups from input model: 0.500 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16472 ( 328) hydrogen bonds : angle 6.46707 ( 972) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.57748 ( 8) covalent geometry : bond 0.01458 ( 8538) covalent geometry : angle 0.72706 (11520) *********************** 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 : 1.009 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: 0.2820 time to fit residues: 44.7765 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 : 0.969 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.166721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143359 restraints weight = 10965.975| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.01 r_work: 0.3647 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 8542 Z= 0.117 Angle : 0.497 6.453 11528 Z= 0.249 Chirality : 0.044 0.157 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.372 94.877 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 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 328) hydrogen bonds : angle 4.61223 ( 972) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.57589 ( 8) covalent geometry : bond 0.00280 ( 8538) covalent geometry : angle 0.49703 (11520) *********************** 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 : 0.975 Fit side-chains REVERT: A 637 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6953 (tt0) REVERT: C 634 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7352 (mm-30) outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.2597 time to fit residues: 49.9510 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 : 1.000 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 59 optimal weight: 0.0070 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.146743 restraints weight = 11084.954| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.02 r_work: 0.3690 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8542 Z= 0.084 Angle : 0.463 6.835 11528 Z= 0.229 Chirality : 0.042 0.144 1284 Planarity : 0.003 0.035 1422 Dihedral : 9.294 85.092 1266 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.24 % Allowed : 15.88 % Favored : 81.88 % 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: 1.00 (0.26), residues: 438 sheet: -1.02 (0.37), residues: 166 loop : -1.14 (0.28), residues: 440 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 0.007 0.001 PHE D 659 TYR 0.009 0.001 TYR C 673 ARG 0.005 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02435 ( 328) hydrogen bonds : angle 4.32501 ( 972) SS BOND : bond 0.00069 ( 4) SS BOND : angle 0.31958 ( 8) covalent geometry : bond 0.00193 ( 8538) covalent geometry : angle 0.46323 (11520) *********************** 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 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.002 Fit side-chains REVERT: A 637 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6970 (tt0) REVERT: A 708 MET cc_start: 0.8095 (mtt) cc_final: 0.7812 (mtt) REVERT: B 414 MET cc_start: 0.6192 (pmm) cc_final: 0.5684 (mpp) REVERT: C 634 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7143 (mm-30) outliers start: 20 outliers final: 13 residues processed: 158 average time/residue: 0.2643 time to fit residues: 54.8722 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL 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 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 419 GLU 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 74 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 0.0040 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.165615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142437 restraints weight = 11012.756| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.00 r_work: 0.3635 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1257 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= 0.127 Angle : 0.510 7.089 11528 Z= 0.251 Chirality : 0.044 0.201 1284 Planarity : 0.004 0.037 1422 Dihedral : 8.736 88.801 1266 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.46 % Allowed : 17.00 % Favored : 80.54 % 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: -0.38 (0.26), residues: 1044 helix: 0.90 (0.26), residues: 438 sheet: -0.97 (0.39), residues: 158 loop : -1.08 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.001 0.001 HIS B 412 PHE 0.018 0.002 PHE A 438 TYR 0.012 0.001 TYR B 405 ARG 0.005 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 328) hydrogen bonds : angle 4.31593 ( 972) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.38841 ( 8) covalent geometry : bond 0.00307 ( 8538) covalent geometry : angle 0.50990 (11520) *********************** 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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.029 Fit side-chains REVERT: A 458 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6963 (mmtm) REVERT: A 637 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7015 (tt0) REVERT: B 414 MET cc_start: 0.6173 (pmm) cc_final: 0.5742 (mpp) REVERT: C 634 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7393 (mm-30) REVERT: D 435 HIS cc_start: 0.6063 (m90) cc_final: 0.5592 (m90) outliers start: 22 outliers final: 17 residues processed: 151 average time/residue: 0.2579 time to fit residues: 51.0321 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 401 LEU 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 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 78 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.166520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143340 restraints weight = 11026.241| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.01 r_work: 0.3659 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1390 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= 0.108 Angle : 0.485 6.704 11528 Z= 0.242 Chirality : 0.044 0.214 1284 Planarity : 0.003 0.037 1422 Dihedral : 7.786 89.511 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 17.11 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1044 helix: 1.05 (0.26), residues: 434 sheet: -0.91 (0.38), residues: 158 loop : -1.10 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.001 0.000 HIS C 435 PHE 0.009 0.001 PHE D 659 TYR 0.009 0.001 TYR B 673 ARG 0.005 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 328) hydrogen bonds : angle 4.21861 ( 972) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.44551 ( 8) covalent geometry : bond 0.00257 ( 8538) covalent geometry : angle 0.48548 (11520) *********************** 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.026 Fit side-chains REVERT: B 414 MET cc_start: 0.6243 (pmm) cc_final: 0.5779 (mpp) REVERT: D 435 HIS cc_start: 0.5959 (m90) cc_final: 0.5469 (m90) outliers start: 23 outliers final: 18 residues processed: 153 average time/residue: 0.2497 time to fit residues: 50.5530 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 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 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 754 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.168056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145204 restraints weight = 10943.613| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.99 r_work: 0.3666 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.091 Angle : 0.459 6.360 11528 Z= 0.232 Chirality : 0.043 0.196 1284 Planarity : 0.003 0.036 1422 Dihedral : 6.917 85.731 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.57 % Allowed : 17.56 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.26), residues: 1044 helix: 1.16 (0.26), residues: 434 sheet: -0.82 (0.38), residues: 158 loop : -1.08 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.001 0.000 HIS C 435 PHE 0.019 0.001 PHE A 438 TYR 0.008 0.001 TYR B 673 ARG 0.007 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02332 ( 328) hydrogen bonds : angle 4.15982 ( 972) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.22789 ( 8) covalent geometry : bond 0.00214 ( 8538) covalent geometry : angle 0.45913 (11520) *********************** 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.947 Fit side-chains REVERT: B 414 MET cc_start: 0.6223 (pmm) cc_final: 0.5799 (mpp) REVERT: D 435 HIS cc_start: 0.5901 (m90) cc_final: 0.5423 (m90) outliers start: 23 outliers final: 19 residues processed: 152 average time/residue: 0.2510 time to fit residues: 50.7999 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN D 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142911 restraints weight = 11078.665| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.01 r_work: 0.3642 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.115 Angle : 0.487 6.908 11528 Z= 0.247 Chirality : 0.044 0.225 1284 Planarity : 0.004 0.037 1422 Dihedral : 6.967 89.244 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.68 % Allowed : 17.34 % Favored : 79.98 % 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: -0.19 (0.26), residues: 1044 helix: 1.11 (0.26), residues: 434 sheet: -0.81 (0.39), residues: 158 loop : -1.05 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.001 0.000 HIS C 435 PHE 0.009 0.001 PHE D 659 TYR 0.010 0.001 TYR B 405 ARG 0.006 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02611 ( 328) hydrogen bonds : angle 4.18458 ( 972) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.45603 ( 8) covalent geometry : bond 0.00278 ( 8538) covalent geometry : angle 0.48668 (11520) *********************** 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.106 Fit side-chains REVERT: B 414 MET cc_start: 0.6237 (pmm) cc_final: 0.5811 (mpp) outliers start: 24 outliers final: 21 residues processed: 153 average time/residue: 0.2639 time to fit residues: 53.3935 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 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 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.165218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141898 restraints weight = 11110.275| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.01 r_work: 0.3627 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8542 Z= 0.129 Angle : 0.508 7.330 11528 Z= 0.258 Chirality : 0.044 0.223 1284 Planarity : 0.004 0.037 1422 Dihedral : 7.172 93.015 1266 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.80 % Allowed : 18.01 % Favored : 79.19 % 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: -0.23 (0.26), residues: 1044 helix: 1.08 (0.26), residues: 432 sheet: -0.88 (0.38), residues: 158 loop : -1.05 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.001 0.000 HIS C 435 PHE 0.019 0.002 PHE C 438 TYR 0.010 0.001 TYR B 405 ARG 0.007 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 328) hydrogen bonds : angle 4.20285 ( 972) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.94147 ( 8) covalent geometry : bond 0.00311 ( 8538) covalent geometry : angle 0.50767 (11520) *********************** 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 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.901 Fit side-chains REVERT: B 414 MET cc_start: 0.6209 (pmm) cc_final: 0.5793 (mpp) outliers start: 25 outliers final: 22 residues processed: 148 average time/residue: 0.2642 time to fit residues: 51.1426 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR 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 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 754 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143139 restraints weight = 11116.093| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.00 r_work: 0.3645 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.111 Angle : 0.487 7.041 11528 Z= 0.247 Chirality : 0.044 0.250 1284 Planarity : 0.004 0.037 1422 Dihedral : 7.034 91.818 1266 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % 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: -0.23 (0.26), residues: 1044 helix: 1.11 (0.26), residues: 434 sheet: -0.94 (0.37), residues: 166 loop : -1.06 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE D 659 TYR 0.008 0.001 TYR B 405 ARG 0.008 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 328) hydrogen bonds : angle 4.16875 ( 972) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.41044 ( 8) covalent geometry : bond 0.00266 ( 8538) covalent geometry : angle 0.48728 (11520) *********************** 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 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.077 Fit side-chains REVERT: B 414 MET cc_start: 0.6208 (pmm) cc_final: 0.5306 (mpp) outliers start: 22 outliers final: 20 residues processed: 144 average time/residue: 0.2735 time to fit residues: 52.2988 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 503 MET 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 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 666 VAL Chi-restraints excluded: chain D residue 693 VAL 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 43 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139696 restraints weight = 11011.185| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.99 r_work: 0.3609 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1802 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= 0.164 Angle : 0.546 8.138 11528 Z= 0.277 Chirality : 0.046 0.225 1284 Planarity : 0.004 0.039 1422 Dihedral : 7.537 97.233 1266 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.46 % Allowed : 18.68 % 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 (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: 0.93 (0.26), residues: 432 sheet: -1.02 (0.38), residues: 158 loop : -1.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.002 0.001 HIS B 412 PHE 0.023 0.002 PHE A 438 TYR 0.013 0.001 TYR B 405 ARG 0.008 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 328) hydrogen bonds : angle 4.28039 ( 972) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.65870 ( 8) covalent geometry : bond 0.00399 ( 8538) covalent geometry : angle 0.54579 (11520) ********************** 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 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.029 Fit side-chains REVERT: B 414 MET cc_start: 0.6165 (pmm) cc_final: 0.5250 (mpp) REVERT: D 634 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6623 (tp30) outliers start: 22 outliers final: 20 residues processed: 140 average time/residue: 0.2683 time to fit residues: 50.4135 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 503 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.166747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143493 restraints weight = 11149.883| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.05 r_work: 0.3635 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.108 Angle : 0.504 9.663 11528 Z= 0.254 Chirality : 0.044 0.169 1284 Planarity : 0.004 0.038 1422 Dihedral : 7.168 92.747 1266 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.01 % Allowed : 19.35 % Favored : 78.64 % 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: -0.28 (0.26), residues: 1044 helix: 1.09 (0.26), residues: 432 sheet: -1.03 (0.38), residues: 162 loop : -1.08 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.001 0.000 HIS C 412 PHE 0.020 0.001 PHE A 438 TYR 0.008 0.001 TYR B 673 ARG 0.008 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02570 ( 328) hydrogen bonds : angle 4.18581 ( 972) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.49355 ( 8) covalent geometry : bond 0.00257 ( 8538) covalent geometry : angle 0.50376 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5046.48 seconds wall clock time: 88 minutes 25.45 seconds (5305.45 seconds total)