Starting phenix.real_space_refine on Sun May 11 21:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpc_29361/05_2025/8fpc_29361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpc_29361/05_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_29361/05_2025/8fpc_29361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpc_29361/05_2025/8fpc_29361.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpc_29361/05_2025/8fpc_29361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpc_29361/05_2025/8fpc_29361.cif" } resolution = 2.78 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.97, per 1000 atoms: 0.71 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: 2.07 Conformation dependent library (CDL) restraints added in 945.8 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 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: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.585A 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: 2.20 Time building geometry restraints manager: 2.42 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: 0.02 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: 3.640 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.100 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- 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 : 5.65 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 (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: -0.03 (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 TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.001 PHE C 495 TYR 0.018 0.001 TYR C 673 ARG 0.014 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.17550 ( 334) hydrogen bonds : angle 6.44527 ( 954) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.24939 ( 8) covalent geometry : bond 0.01454 ( 8538) covalent geometry : angle 0.71560 (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 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.078 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 140 average time/residue: 1.6032 time to fit residues: 235.7183 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 : 0.941 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116495 restraints weight = 9568.089| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.12 r_work: 0.3187 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.109 Angle : 0.496 6.289 11528 Z= 0.248 Chirality : 0.042 0.128 1284 Planarity : 0.004 0.037 1422 Dihedral : 11.210 97.224 1290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.47 % Allowed : 24.50 % Favored : 72.04 % 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: 0.15 (0.26), residues: 1044 helix: 1.42 (0.26), residues: 434 sheet: -0.39 (0.37), residues: 174 loop : -1.02 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE C 495 TYR 0.011 0.001 TYR A 673 ARG 0.006 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 334) hydrogen bonds : angle 4.78421 ( 954) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.25007 ( 8) covalent geometry : bond 0.00255 ( 8538) covalent geometry : angle 0.49644 (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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.004 Fit side-chains REVERT: B 637 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: B 675 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7491 (ptm-80) REVERT: C 453 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5765 (ttm-80) REVERT: D 458 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7285 (mppt) REVERT: D 675 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7604 (ptm-80) REVERT: D 719 ASP cc_start: 0.8554 (p0) cc_final: 0.8295 (p0) REVERT: D 761 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7529 (pttp) outliers start: 31 outliers final: 12 residues processed: 146 average time/residue: 1.5290 time to fit residues: 234.3918 Evaluate side-chains 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.141700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113627 restraints weight = 9795.333| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.15 r_work: 0.3161 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8542 Z= 0.142 Angle : 0.529 6.749 11528 Z= 0.262 Chirality : 0.044 0.129 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.887 96.043 1277 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.59 % Allowed : 24.05 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.26), residues: 1044 helix: 1.34 (0.26), residues: 434 sheet: -0.47 (0.36), residues: 174 loop : -1.07 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.001 HIS D 412 PHE 0.013 0.002 PHE C 495 TYR 0.010 0.001 TYR D 711 ARG 0.006 0.001 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 334) hydrogen bonds : angle 4.70705 ( 954) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.40593 ( 8) covalent geometry : bond 0.00346 ( 8538) covalent geometry : angle 0.52886 (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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.925 Fit side-chains REVERT: B 453 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7471 (ttt-90) REVERT: B 675 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7635 (ptm-80) REVERT: B 761 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7711 (pttp) REVERT: C 453 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5960 (ttm-80) REVERT: C 755 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: D 675 ARG cc_start: 0.8067 (ptp90) cc_final: 0.7675 (ptm-80) REVERT: D 715 ARG cc_start: 0.6810 (mmm-85) cc_final: 0.6052 (mpt180) REVERT: D 719 ASP cc_start: 0.8577 (p0) cc_final: 0.8351 (p0) outliers start: 41 outliers final: 17 residues processed: 154 average time/residue: 1.5252 time to fit residues: 246.6145 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 755 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 651 ASP 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 23 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.142878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115172 restraints weight = 9646.398| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.09 r_work: 0.3150 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8542 Z= 0.138 Angle : 0.524 6.915 11528 Z= 0.259 Chirality : 0.044 0.126 1284 Planarity : 0.003 0.029 1422 Dihedral : 10.808 95.175 1277 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.59 % Allowed : 24.72 % Favored : 70.69 % 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: 0.04 (0.25), residues: 1044 helix: 1.33 (0.26), residues: 434 sheet: -0.44 (0.37), residues: 174 loop : -1.09 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS D 412 PHE 0.014 0.002 PHE B 438 TYR 0.009 0.001 TYR A 673 ARG 0.006 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 334) hydrogen bonds : angle 4.62908 ( 954) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.42095 ( 8) covalent geometry : bond 0.00335 ( 8538) covalent geometry : angle 0.52358 (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 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.998 Fit side-chains REVERT: A 407 MET cc_start: 0.8692 (mpp) cc_final: 0.8468 (mtt) REVERT: B 453 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7421 (ttt-90) REVERT: B 761 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7738 (pttp) REVERT: C 418 ASN cc_start: 0.7846 (m-40) cc_final: 0.7598 (m110) REVERT: C 453 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5991 (ttm-80) REVERT: C 748 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 755 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: D 454 ASP cc_start: 0.7758 (t0) cc_final: 0.7304 (t0) REVERT: D 661 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7898 (mtt180) REVERT: D 719 ASP cc_start: 0.8539 (p0) cc_final: 0.8330 (p0) REVERT: D 761 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7747 (pttp) outliers start: 41 outliers final: 23 residues processed: 151 average time/residue: 1.5519 time to fit residues: 246.0683 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 630 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 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 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 457 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.144485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116972 restraints weight = 9564.535| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.09 r_work: 0.3197 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.106 Angle : 0.501 6.569 11528 Z= 0.247 Chirality : 0.042 0.129 1284 Planarity : 0.003 0.032 1422 Dihedral : 10.238 93.003 1275 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.91 % Allowed : 25.50 % 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 (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: 1.48 (0.26), residues: 434 sheet: -0.42 (0.36), residues: 174 loop : -1.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE D 438 TYR 0.008 0.001 TYR D 732 ARG 0.008 0.001 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 334) hydrogen bonds : angle 4.50178 ( 954) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.30946 ( 8) covalent geometry : bond 0.00252 ( 8538) covalent geometry : angle 0.50134 (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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.037 Fit side-chains REVERT: B 453 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7385 (ttt-90) REVERT: B 761 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7711 (pttp) REVERT: C 418 ASN cc_start: 0.7789 (m-40) cc_final: 0.7546 (m110) REVERT: C 453 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5939 (ttm-80) REVERT: C 748 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 755 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: D 454 ASP cc_start: 0.7646 (t0) cc_final: 0.7263 (t0) REVERT: D 661 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7806 (mtt180) outliers start: 35 outliers final: 21 residues processed: 149 average time/residue: 1.6245 time to fit residues: 253.8208 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 436 CYS 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 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 498 LEU Chi-restraints excluded: chain D residue 651 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113274 restraints weight = 9706.115| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.08 r_work: 0.3134 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8542 Z= 0.197 Angle : 0.586 7.884 11528 Z= 0.292 Chirality : 0.046 0.145 1284 Planarity : 0.004 0.041 1422 Dihedral : 10.980 97.006 1274 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.81 % Allowed : 25.28 % 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 (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: -0.08 (0.25), residues: 1044 helix: 1.20 (0.25), residues: 432 sheet: -0.45 (0.36), residues: 174 loop : -1.13 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.016 0.002 PHE A 495 TYR 0.012 0.002 TYR B 421 ARG 0.008 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 334) hydrogen bonds : angle 4.74138 ( 954) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.54324 ( 8) covalent geometry : bond 0.00485 ( 8538) covalent geometry : angle 0.58621 (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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.915 Fit side-chains REVERT: A 634 GLU cc_start: 0.7462 (tp30) cc_final: 0.7197 (tp30) REVERT: B 453 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7472 (ttt-90) REVERT: B 761 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (pttp) REVERT: C 418 ASN cc_start: 0.7956 (m-40) cc_final: 0.7708 (m110) REVERT: C 453 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6038 (ttm-80) REVERT: C 748 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 755 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: D 454 ASP cc_start: 0.7817 (t0) cc_final: 0.7330 (t0) REVERT: D 761 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7767 (pttp) outliers start: 43 outliers final: 25 residues processed: 149 average time/residue: 1.5359 time to fit residues: 239.8921 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 736 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS 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 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 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 498 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.142498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114733 restraints weight = 9745.708| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.10 r_work: 0.3162 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.125 Angle : 0.532 7.037 11528 Z= 0.263 Chirality : 0.043 0.137 1284 Planarity : 0.004 0.044 1422 Dihedral : 10.584 94.885 1273 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.70 % Allowed : 24.83 % Favored : 70.47 % 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: 0.03 (0.26), residues: 1044 helix: 1.36 (0.26), residues: 434 sheet: -0.47 (0.36), residues: 174 loop : -1.11 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.001 PHE D 438 TYR 0.006 0.001 TYR C 768 ARG 0.010 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 334) hydrogen bonds : angle 4.55859 ( 954) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.36890 ( 8) covalent geometry : bond 0.00302 ( 8538) covalent geometry : angle 0.53211 (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 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.940 Fit side-chains REVERT: B 453 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7430 (ttt-90) REVERT: B 637 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: B 761 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7722 (pttp) REVERT: C 418 ASN cc_start: 0.7885 (m-40) cc_final: 0.7618 (m110) REVERT: C 453 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6031 (ttm-80) REVERT: C 484 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8497 (m) REVERT: C 748 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8558 (mp) REVERT: C 755 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: D 454 ASP cc_start: 0.7677 (t0) cc_final: 0.7232 (t0) REVERT: D 661 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7744 (mtt90) REVERT: D 761 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7736 (pttp) outliers start: 42 outliers final: 24 residues processed: 148 average time/residue: 1.5608 time to fit residues: 242.3989 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 436 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 637 GLU 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 498 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113585 restraints weight = 9757.904| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.08 r_work: 0.3145 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8542 Z= 0.161 Angle : 0.563 7.785 11528 Z= 0.279 Chirality : 0.045 0.151 1284 Planarity : 0.004 0.048 1422 Dihedral : 10.716 96.417 1273 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.59 % Allowed : 24.72 % Favored : 70.69 % 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: -0.06 (0.25), residues: 1044 helix: 1.25 (0.25), residues: 432 sheet: -0.47 (0.36), residues: 174 loop : -1.15 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.013 0.002 PHE A 495 TYR 0.013 0.001 TYR A 673 ARG 0.011 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 334) hydrogen bonds : angle 4.64361 ( 954) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.44818 ( 8) covalent geometry : bond 0.00395 ( 8538) covalent geometry : angle 0.56283 (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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 1.019 Fit side-chains REVERT: B 453 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7464 (ttt-90) REVERT: B 637 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 761 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7757 (pttp) REVERT: C 418 ASN cc_start: 0.7922 (m-40) cc_final: 0.7676 (m110) REVERT: C 453 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.5997 (ttm-80) REVERT: C 748 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8542 (mp) REVERT: D 454 ASP cc_start: 0.7663 (t0) cc_final: 0.7220 (t0) REVERT: D 761 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7745 (pttp) outliers start: 41 outliers final: 26 residues processed: 146 average time/residue: 1.5968 time to fit residues: 244.2613 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 637 GLU 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 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 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.141726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114137 restraints weight = 9869.240| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.09 r_work: 0.3140 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8542 Z= 0.153 Angle : 0.563 7.554 11528 Z= 0.280 Chirality : 0.044 0.176 1284 Planarity : 0.004 0.052 1422 Dihedral : 10.482 96.594 1272 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.36 % Allowed : 24.72 % Favored : 70.92 % 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: -0.12 (0.25), residues: 1044 helix: 1.21 (0.25), residues: 434 sheet: -0.53 (0.36), residues: 174 loop : -1.18 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.013 0.002 PHE D 438 TYR 0.008 0.001 TYR D 421 ARG 0.012 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 334) hydrogen bonds : angle 4.62066 ( 954) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.42630 ( 8) covalent geometry : bond 0.00374 ( 8538) covalent geometry : angle 0.56347 (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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.035 Fit side-chains REVERT: B 453 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7442 (ttt-90) REVERT: B 637 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 761 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7743 (pttp) REVERT: C 418 ASN cc_start: 0.7908 (m-40) cc_final: 0.7653 (m110) REVERT: C 453 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.5963 (ttm-80) REVERT: C 748 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 755 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: D 454 ASP cc_start: 0.7645 (t0) cc_final: 0.7186 (t0) REVERT: D 761 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7722 (pttp) outliers start: 39 outliers final: 28 residues processed: 145 average time/residue: 1.6288 time to fit residues: 248.0622 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 436 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 637 GLU 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 498 LEU Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113986 restraints weight = 9788.133| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.14 r_work: 0.3150 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1374 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= 0.121 Angle : 0.532 6.977 11528 Z= 0.264 Chirality : 0.043 0.211 1284 Planarity : 0.004 0.055 1422 Dihedral : 9.907 93.786 1272 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.69 % Allowed : 25.39 % Favored : 70.92 % 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: 0.02 (0.26), residues: 1044 helix: 1.36 (0.26), residues: 434 sheet: -0.53 (0.36), residues: 174 loop : -1.11 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE A 495 TYR 0.021 0.001 TYR C 673 ARG 0.013 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 334) hydrogen bonds : angle 4.51552 ( 954) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.33705 ( 8) covalent geometry : bond 0.00290 ( 8538) covalent geometry : angle 0.53226 (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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.932 Fit side-chains REVERT: B 453 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7416 (ttt-90) REVERT: B 637 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: B 761 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7673 (pttp) REVERT: C 418 ASN cc_start: 0.7852 (m-40) cc_final: 0.7600 (m110) REVERT: C 453 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5974 (ttm-80) REVERT: C 748 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 755 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: D 454 ASP cc_start: 0.7620 (t0) cc_final: 0.7244 (t0) REVERT: D 661 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7733 (mtt90) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 1.5792 time to fit residues: 240.0914 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 474 ILE 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 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 498 LEU Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112589 restraints weight = 9924.704| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.16 r_work: 0.3139 rms_B_bonded: 2.67 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: 0.8460 moved from start: 0.1391 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= 0.142 Angle : 0.548 7.609 11528 Z= 0.274 Chirality : 0.044 0.192 1284 Planarity : 0.004 0.055 1422 Dihedral : 9.921 94.224 1272 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.03 % Allowed : 25.50 % Favored : 70.47 % 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: -0.05 (0.25), residues: 1044 helix: 1.27 (0.25), residues: 434 sheet: -0.53 (0.36), residues: 174 loop : -1.12 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.012 0.002 PHE D 438 TYR 0.009 0.001 TYR A 673 ARG 0.013 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 334) hydrogen bonds : angle 4.57836 ( 954) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.37229 ( 8) covalent geometry : bond 0.00345 ( 8538) covalent geometry : angle 0.54799 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6868.55 seconds wall clock time: 119 minutes 3.14 seconds (7143.14 seconds total)