Starting phenix.real_space_refine on Fri Aug 22 22:58:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpc_29361/08_2025/8fpc_29361.cif" } resolution = 2.78 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 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 8400 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.96, per 1000 atoms: 0.23 Number of scatterers: 8400 At special positions: 0 Unit cell: (117.189, 89.3255, 84.4085, 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 1616 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: 0.48 Conformation dependent library (CDL) restraints added in 378.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 46 helices and 21 sheets defined 43.1% alpha, 13.3% 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: 3.585A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.553A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.746A 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 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.962A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.521A 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 removed outlier: 3.563A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 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 416 through 419 removed outlier: 3.780A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.611A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.760A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.880A 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 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 440 through 444 removed outlier: 6.381A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.053A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.511A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.850A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.560A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.018A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.589A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.301A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.989A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.485A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.854A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 454 removed outlier: 3.639A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.060A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.690A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 954 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: 0.92 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2630 1.35 - 1.47: 2040 1.47 - 1.60: 3724 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 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 1.46e+02 bond pdb=" C5 CYZ A1302 " pdb=" C6 CYZ A1302 " ideal model delta sigma weight residual 1.553 1.329 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11289 1.90 - 3.80: 142 3.80 - 5.70: 44 5.70 - 7.60: 27 7.60 - 9.51: 18 Bond angle restraints: 11520 Sorted by residual: angle pdb=" N VAL D 488 " pdb=" CA VAL D 488 " pdb=" C VAL D 488 " ideal model delta sigma weight residual 113.71 110.27 3.44 9.50e-01 1.11e+00 1.31e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.26 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.16 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.14 -9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.13 -9.38 3.00e+00 1.11e-01 9.77e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 4647 22.59 - 45.18: 476 45.18 - 67.76: 96 67.76 - 90.35: 17 90.35 - 112.94: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual -86.00 -166.14 80.14 1 1.00e+01 1.00e-02 7.96e+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 93.00 169.63 -76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 163.98 -70.98 1 1.00e+01 1.00e-02 6.47e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1172 0.085 - 0.170: 96 0.170 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.424: 16 Chirality restraints: 1284 Sorted by residual: 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 2.89 0.42 2.00e-01 2.50e+01 4.49e+00 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 2.89 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 684 " -0.125 9.50e-02 1.11e+02 5.66e-02 2.58e+00 pdb=" NE ARG D 684 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 684 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 684 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 684 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 684 " 0.120 9.50e-02 1.11e+02 5.41e-02 2.33e+00 pdb=" NE ARG B 684 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 684 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 684 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 684 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 737 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1453 2.77 - 3.30: 7597 3.30 - 3.83: 14189 3.83 - 4.37: 16997 4.37 - 4.90: 29250 Nonbonded interactions: 69486 Sorted by model distance: nonbonded pdb=" OG SER B 654 " pdb=" O HOH B1401 " model vdw 2.235 3.040 nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR D 398 " pdb=" OE2 GLU D 466 " model vdw 2.295 3.040 nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.302 3.040 nonbonded pdb=" OG SER B 510 " pdb=" O ARG B 628 " model vdw 2.309 3.040 ... (remaining 69481 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: 0.01 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: 2.670 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.242 8542 Z= 0.725 Angle : 0.715 9.506 11528 Z= 0.307 Chirality : 0.062 0.424 1284 Planarity : 0.004 0.057 1422 Dihedral : 18.670 112.941 3288 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 27.74 % Favored : 69.91 % 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: -0.03 (0.25), residues: 1044 helix: 1.25 (0.26), residues: 432 sheet: -0.53 (0.36), residues: 174 loop : -1.07 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 684 TYR 0.018 0.001 TYR C 673 PHE 0.011 0.001 PHE C 495 TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.01454 ( 8538) covalent geometry : angle 0.71560 (11520) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.24939 ( 8) hydrogen bonds : bond 0.17550 ( 334) hydrogen bonds : angle 6.44527 ( 954) *********************** 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 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.351 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 140 average time/residue: 0.6325 time to fit residues: 92.7592 Evaluate side-chains 133 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114708 restraints weight = 9659.192| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.13 r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0799 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= 0.126 Angle : 0.516 6.322 11528 Z= 0.257 Chirality : 0.043 0.139 1284 Planarity : 0.004 0.036 1422 Dihedral : 11.319 98.131 1290 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.25 % Allowed : 23.60 % Favored : 72.15 % 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: 0.09 (0.26), residues: 1044 helix: 1.36 (0.26), residues: 434 sheet: -0.43 (0.37), residues: 174 loop : -1.04 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 684 TYR 0.010 0.001 TYR A 673 PHE 0.012 0.001 PHE C 495 TRP 0.006 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8538) covalent geometry : angle 0.51576 (11520) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.30920 ( 8) hydrogen bonds : bond 0.03723 ( 334) hydrogen bonds : angle 4.83074 ( 954) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.213 Fit side-chains REVERT: B 637 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: B 675 ARG cc_start: 0.7909 (ptp90) cc_final: 0.7569 (ptm-80) REVERT: C 453 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.5819 (ttm-80) REVERT: D 675 ARG cc_start: 0.8026 (ptp90) cc_final: 0.7626 (ptm-80) REVERT: D 719 ASP cc_start: 0.8582 (p0) cc_final: 0.8321 (p0) REVERT: D 761 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7568 (pttp) outliers start: 38 outliers final: 14 residues processed: 151 average time/residue: 0.6546 time to fit residues: 103.6579 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114200 restraints weight = 9591.529| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.12 r_work: 0.3161 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1023 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= 0.129 Angle : 0.517 6.560 11528 Z= 0.256 Chirality : 0.043 0.129 1284 Planarity : 0.003 0.029 1422 Dihedral : 10.830 95.649 1277 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.25 % Allowed : 24.16 % Favored : 71.59 % 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: 0.06 (0.26), residues: 1044 helix: 1.36 (0.26), residues: 434 sheet: -0.49 (0.37), residues: 174 loop : -1.06 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 715 TYR 0.009 0.001 TYR D 711 PHE 0.012 0.001 PHE C 495 TRP 0.007 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8538) covalent geometry : angle 0.51710 (11520) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.35975 ( 8) hydrogen bonds : bond 0.03495 ( 334) hydrogen bonds : angle 4.67033 ( 954) *********************** 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 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.305 Fit side-chains REVERT: B 453 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7438 (ttt-90) REVERT: B 675 ARG cc_start: 0.7965 (ptp90) cc_final: 0.7593 (ptm-80) REVERT: B 761 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7708 (pttp) REVERT: C 418 ASN cc_start: 0.7831 (m-40) cc_final: 0.7560 (m110) REVERT: C 453 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.5867 (ttm-80) REVERT: C 748 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8519 (mp) REVERT: C 755 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: D 454 ASP cc_start: 0.7778 (t0) cc_final: 0.7363 (t0) REVERT: D 675 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7655 (ptm-80) REVERT: D 715 ARG cc_start: 0.6786 (mmm-85) cc_final: 0.6048 (mpt180) REVERT: D 719 ASP cc_start: 0.8555 (p0) cc_final: 0.8320 (p0) outliers start: 38 outliers final: 16 residues processed: 149 average time/residue: 0.6631 time to fit residues: 103.8845 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 742 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115127 restraints weight = 9807.421| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.16 r_work: 0.3184 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1113 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= 0.105 Angle : 0.494 6.301 11528 Z= 0.243 Chirality : 0.042 0.125 1284 Planarity : 0.003 0.028 1422 Dihedral : 10.377 92.952 1276 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.58 % Allowed : 25.28 % Favored : 71.14 % 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: 0.16 (0.26), residues: 1044 helix: 1.48 (0.26), residues: 434 sheet: -0.49 (0.36), residues: 174 loop : -1.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 684 TYR 0.010 0.001 TYR A 673 PHE 0.012 0.001 PHE B 438 TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8538) covalent geometry : angle 0.49362 (11520) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.28352 ( 8) hydrogen bonds : bond 0.03016 ( 334) hydrogen bonds : angle 4.50708 ( 954) *********************** 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 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.224 Fit side-chains REVERT: A 407 MET cc_start: 0.8696 (mpp) cc_final: 0.8492 (mtt) REVERT: B 453 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7399 (ttt-90) REVERT: B 675 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7510 (ptm-80) REVERT: B 761 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7690 (pttp) REVERT: C 418 ASN cc_start: 0.7797 (m-40) cc_final: 0.7543 (m110) REVERT: C 453 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5947 (ttm-80) REVERT: C 748 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 755 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: D 454 ASP cc_start: 0.7758 (t0) cc_final: 0.7363 (t0) REVERT: D 661 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7896 (mtt180) REVERT: D 669 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: D 675 ARG cc_start: 0.8023 (ptp90) cc_final: 0.7592 (ptm-80) REVERT: D 715 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.5946 (mmt-90) REVERT: D 719 ASP cc_start: 0.8486 (p0) cc_final: 0.8266 (p0) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 0.6440 time to fit residues: 99.9532 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 742 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.0000 chunk 53 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121490 restraints weight = 9751.036| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.11 r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.087 Angle : 0.479 7.219 11528 Z= 0.233 Chirality : 0.042 0.199 1284 Planarity : 0.003 0.029 1422 Dihedral : 8.849 84.361 1275 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.13 % Allowed : 26.51 % Favored : 70.36 % 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: 0.34 (0.26), residues: 1044 helix: 1.70 (0.26), residues: 434 sheet: -0.59 (0.38), residues: 166 loop : -0.93 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 684 TYR 0.007 0.001 TYR D 732 PHE 0.007 0.001 PHE B 495 TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8538) covalent geometry : angle 0.47913 (11520) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.23920 ( 8) hydrogen bonds : bond 0.02432 ( 334) hydrogen bonds : angle 4.34729 ( 954) *********************** 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: 28 poor density : 127 time to evaluate : 0.270 Fit side-chains REVERT: B 453 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7306 (ttt-90) REVERT: B 715 ARG cc_start: 0.6940 (mmm-85) cc_final: 0.6720 (mmm-85) REVERT: B 761 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7686 (pttp) REVERT: C 418 ASN cc_start: 0.7735 (m-40) cc_final: 0.7471 (m110) REVERT: C 453 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5912 (ttm-80) REVERT: C 748 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8537 (mp) REVERT: C 755 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: D 458 LYS cc_start: 0.7977 (mptt) cc_final: 0.7347 (mppt) REVERT: D 629 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7029 (ttp) REVERT: D 661 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7733 (mtt90) REVERT: D 715 ARG cc_start: 0.6844 (mmm-85) cc_final: 0.6359 (mpt180) REVERT: D 719 ASP cc_start: 0.8398 (p0) cc_final: 0.8149 (p0) REVERT: D 761 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7756 (pttp) outliers start: 28 outliers final: 10 residues processed: 147 average time/residue: 0.6698 time to fit residues: 103.1043 Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.0030 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115915 restraints weight = 9733.006| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1294 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= 0.110 Angle : 0.500 7.296 11528 Z= 0.246 Chirality : 0.043 0.215 1284 Planarity : 0.004 0.037 1422 Dihedral : 7.649 76.303 1270 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.47 % Allowed : 26.17 % Favored : 70.36 % 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: 0.34 (0.26), residues: 1044 helix: 1.66 (0.26), residues: 434 sheet: -0.46 (0.36), residues: 174 loop : -0.94 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 684 TYR 0.011 0.001 TYR A 673 PHE 0.010 0.001 PHE C 495 TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8538) covalent geometry : angle 0.50043 (11520) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.29001 ( 8) hydrogen bonds : bond 0.02962 ( 334) hydrogen bonds : angle 4.42270 ( 954) *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.334 Fit side-chains REVERT: A 699 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7358 (mmtt) REVERT: B 715 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6740 (mmm-85) REVERT: B 761 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7674 (pttp) REVERT: C 418 ASN cc_start: 0.7769 (m-40) cc_final: 0.7508 (m110) REVERT: C 453 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.5904 (ttm-80) REVERT: C 748 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 755 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: D 458 LYS cc_start: 0.7977 (mptt) cc_final: 0.7370 (mppt) REVERT: D 715 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6128 (mmt-90) REVERT: D 719 ASP cc_start: 0.8434 (p0) cc_final: 0.8222 (p0) REVERT: D 761 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7779 (pttp) outliers start: 31 outliers final: 15 residues processed: 142 average time/residue: 0.7192 time to fit residues: 107.0232 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112988 restraints weight = 9867.597| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.15 r_work: 0.3140 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8542 Z= 0.151 Angle : 0.546 7.258 11528 Z= 0.271 Chirality : 0.045 0.217 1284 Planarity : 0.004 0.044 1422 Dihedral : 7.123 65.161 1269 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.80 % Allowed : 25.62 % Favored : 70.58 % 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: 0.19 (0.26), residues: 1044 helix: 1.48 (0.26), residues: 434 sheet: -0.47 (0.37), residues: 174 loop : -0.99 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 684 TYR 0.009 0.001 TYR B 421 PHE 0.014 0.002 PHE C 495 TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8538) covalent geometry : angle 0.54640 (11520) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.39521 ( 8) hydrogen bonds : bond 0.03558 ( 334) hydrogen bonds : angle 4.56770 ( 954) *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.253 Fit side-chains REVERT: A 407 MET cc_start: 0.8677 (mpp) cc_final: 0.8401 (mtt) REVERT: A 699 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7441 (mmpt) REVERT: B 675 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7657 (ptm-80) REVERT: B 761 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7732 (pttp) REVERT: C 418 ASN cc_start: 0.7845 (m-40) cc_final: 0.7599 (m110) REVERT: C 453 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6020 (ttm-80) REVERT: C 748 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8530 (mp) REVERT: C 755 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: D 714 GLN cc_start: 0.7009 (mm-40) cc_final: 0.5835 (pt0) REVERT: D 761 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7732 (pttp) REVERT: D 768 TYR cc_start: 0.6917 (m-80) cc_final: 0.6704 (m-80) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.7315 time to fit residues: 110.6721 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 38 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113762 restraints weight = 9638.567| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.08 r_work: 0.3155 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8542 Z= 0.166 Angle : 0.557 7.697 11528 Z= 0.278 Chirality : 0.046 0.228 1284 Planarity : 0.004 0.047 1422 Dihedral : 6.556 57.814 1269 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.03 % Allowed : 25.84 % Favored : 70.13 % 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: 0.04 (0.25), residues: 1044 helix: 1.34 (0.25), residues: 434 sheet: -0.50 (0.36), residues: 174 loop : -1.07 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 684 TYR 0.014 0.002 TYR A 673 PHE 0.015 0.002 PHE C 495 TRP 0.007 0.001 TRP C 460 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8538) covalent geometry : angle 0.55689 (11520) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.47512 ( 8) hydrogen bonds : bond 0.03699 ( 334) hydrogen bonds : angle 4.62422 ( 954) *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.249 Fit side-chains REVERT: A 407 MET cc_start: 0.8733 (mpp) cc_final: 0.8519 (mtt) REVERT: A 634 GLU cc_start: 0.7454 (tp30) cc_final: 0.7193 (tp30) REVERT: A 699 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7410 (mmpt) REVERT: B 761 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7749 (pttp) REVERT: C 418 ASN cc_start: 0.7911 (m-40) cc_final: 0.7662 (m110) REVERT: C 453 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6047 (ttm-80) REVERT: C 484 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (m) REVERT: C 748 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 755 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: D 761 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7795 (pttp) outliers start: 36 outliers final: 21 residues processed: 148 average time/residue: 0.6992 time to fit residues: 108.4151 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116800 restraints weight = 9679.885| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.04 r_work: 0.3154 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1422 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= 0.136 Angle : 0.529 7.067 11528 Z= 0.266 Chirality : 0.044 0.177 1284 Planarity : 0.004 0.052 1422 Dihedral : 6.150 57.405 1269 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 26.06 % Favored : 70.58 % 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: 0.09 (0.26), residues: 1044 helix: 1.40 (0.26), residues: 434 sheet: -0.50 (0.37), residues: 174 loop : -1.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 684 TYR 0.007 0.001 TYR B 421 PHE 0.012 0.002 PHE A 495 TRP 0.007 0.001 TRP A 766 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8538) covalent geometry : angle 0.52862 (11520) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.38256 ( 8) hydrogen bonds : bond 0.03333 ( 334) hydrogen bonds : angle 4.55021 ( 954) *********************** 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: 30 poor density : 117 time to evaluate : 0.256 Fit side-chains REVERT: A 407 MET cc_start: 0.8730 (mpp) cc_final: 0.8389 (mtt) REVERT: A 699 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7405 (mmpt) REVERT: B 675 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7673 (ptm-80) REVERT: B 761 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7736 (pttp) REVERT: C 418 ASN cc_start: 0.7889 (m-40) cc_final: 0.7646 (m110) REVERT: C 453 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6034 (ttm-80) REVERT: C 484 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8529 (m) REVERT: C 748 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 755 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: D 761 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7794 (pttp) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 0.6522 time to fit residues: 95.4900 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118893 restraints weight = 9745.220| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8542 Z= 0.102 Angle : 0.493 6.267 11528 Z= 0.249 Chirality : 0.042 0.133 1284 Planarity : 0.004 0.055 1422 Dihedral : 5.671 58.040 1269 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.02 % Allowed : 26.85 % Favored : 70.13 % 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: 0.24 (0.26), residues: 1044 helix: 1.58 (0.26), residues: 434 sheet: -0.49 (0.37), residues: 174 loop : -0.99 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 684 TYR 0.021 0.001 TYR C 673 PHE 0.009 0.001 PHE A 495 TRP 0.007 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8538) covalent geometry : angle 0.49281 (11520) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.25805 ( 8) hydrogen bonds : bond 0.02751 ( 334) hydrogen bonds : angle 4.41657 ( 954) ********************** 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: 27 poor density : 116 time to evaluate : 0.264 Fit side-chains REVERT: A 407 MET cc_start: 0.8699 (mpp) cc_final: 0.8425 (mtt) REVERT: B 761 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7682 (pttp) REVERT: C 418 ASN cc_start: 0.7799 (m-40) cc_final: 0.7563 (m110) REVERT: C 453 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5953 (ttm-80) REVERT: C 484 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (m) REVERT: C 748 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8536 (mp) REVERT: C 755 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: D 453 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8389 (ttp80) REVERT: D 661 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7709 (mtt90) REVERT: D 761 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7785 (pttp) outliers start: 27 outliers final: 16 residues processed: 135 average time/residue: 0.6650 time to fit residues: 94.1722 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 104 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114135 restraints weight = 9767.079| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.12 r_work: 0.3163 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1443 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= 0.134 Angle : 0.533 7.114 11528 Z= 0.268 Chirality : 0.044 0.247 1284 Planarity : 0.004 0.055 1422 Dihedral : 5.857 59.708 1269 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.47 % Allowed : 26.73 % Favored : 69.80 % 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: 0.15 (0.26), residues: 1044 helix: 1.47 (0.26), residues: 434 sheet: -0.48 (0.37), residues: 174 loop : -1.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 684 TYR 0.009 0.001 TYR A 673 PHE 0.012 0.001 PHE A 495 TRP 0.008 0.001 TRP A 766 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8538) covalent geometry : angle 0.53318 (11520) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.35087 ( 8) hydrogen bonds : bond 0.03299 ( 334) hydrogen bonds : angle 4.51406 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.92 seconds wall clock time: 51 minutes 53.35 seconds (3113.35 seconds total)