Starting phenix.real_space_refine on Fri Nov 15 06:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_29361.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_29361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_29361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_29361.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpc_29361/11_2024/8fpc_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-5513/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: 6.61, per 1000 atoms: 0.79 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 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: 1.20 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: 2.35 Time building geometry restraints manager: 2.56 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.910 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- 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 8538 Z= 0.993 Angle : 0.716 9.506 11520 Z= 0.308 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 *********************** 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 : 0.961 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 140 average time/residue: 1.6545 time to fit residues: 242.6774 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 : 0.999 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 8538 Z= 0.161 Angle : 0.496 6.289 11520 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 *********************** 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 : 1.007 Fit side-chains REVERT: B 637 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: B 675 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7486 (ptm-80) REVERT: C 453 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5734 (ttm-80) REVERT: D 458 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7469 (mppt) REVERT: D 675 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7609 (ptm-80) REVERT: D 719 ASP cc_start: 0.8565 (p0) cc_final: 0.8285 (p0) REVERT: D 761 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7540 (pttp) outliers start: 31 outliers final: 12 residues processed: 146 average time/residue: 1.6504 time to fit residues: 253.1339 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 : 1.019 ------------------------------------------------------------------------------- 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 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8538 Z= 0.177 Angle : 0.505 6.314 11520 Z= 0.249 Chirality : 0.043 0.128 1284 Planarity : 0.003 0.037 1422 Dihedral : 10.587 94.129 1277 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.47 % Allowed : 23.94 % 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 (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: 0.14 (0.26), residues: 1044 helix: 1.45 (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 TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS D 412 PHE 0.011 0.001 PHE C 495 TYR 0.010 0.001 TYR D 711 ARG 0.007 0.001 ARG D 715 *********************** 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: 40 poor density : 127 time to evaluate : 1.046 Fit side-chains REVERT: B 453 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7190 (ttt-90) REVERT: B 675 ARG cc_start: 0.7745 (ptp90) cc_final: 0.7507 (ptm-80) REVERT: B 761 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7596 (pttp) REVERT: C 407 MET cc_start: 0.8643 (mtt) cc_final: 0.8423 (mtt) REVERT: C 418 ASN cc_start: 0.7869 (m-40) cc_final: 0.7638 (m110) REVERT: C 453 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5773 (ttm-80) REVERT: C 755 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: D 675 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7596 (ptm-80) REVERT: D 715 ARG cc_start: 0.6835 (mmm-85) cc_final: 0.6276 (mpt180) REVERT: D 719 ASP cc_start: 0.8574 (p0) cc_final: 0.8308 (p0) REVERT: D 768 TYR cc_start: 0.6667 (m-80) cc_final: 0.6294 (m-80) outliers start: 40 outliers final: 15 residues processed: 154 average time/residue: 1.6095 time to fit residues: 260.3537 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL 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 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 95 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8538 Z= 0.172 Angle : 0.503 6.741 11520 Z= 0.248 Chirality : 0.043 0.134 1284 Planarity : 0.003 0.031 1422 Dihedral : 10.207 92.920 1275 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.80 % Allowed : 25.28 % 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: 0.19 (0.26), residues: 1044 helix: 1.50 (0.26), residues: 434 sheet: -0.43 (0.37), residues: 174 loop : -1.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.002 0.001 HIS D 412 PHE 0.012 0.001 PHE B 438 TYR 0.010 0.001 TYR A 673 ARG 0.007 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.019 Fit side-chains REVERT: A 407 MET cc_start: 0.8739 (mpp) cc_final: 0.8504 (mtt) REVERT: B 453 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7191 (ttt-90) REVERT: B 675 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7457 (ptm-80) REVERT: B 761 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7624 (pttp) REVERT: C 418 ASN cc_start: 0.7856 (m-40) cc_final: 0.7631 (m110) REVERT: C 453 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5853 (ttm-80) REVERT: C 748 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8642 (mp) REVERT: C 755 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: D 454 ASP cc_start: 0.7671 (t0) cc_final: 0.7321 (t0) REVERT: D 675 ARG cc_start: 0.7878 (ptp90) cc_final: 0.7577 (ptm-80) REVERT: D 715 ARG cc_start: 0.6789 (mmm-85) cc_final: 0.6164 (mmt-90) REVERT: D 719 ASP cc_start: 0.8525 (p0) cc_final: 0.8276 (p0) outliers start: 34 outliers final: 19 residues processed: 150 average time/residue: 1.5832 time to fit residues: 249.5993 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8538 Z= 0.150 Angle : 0.498 7.146 11520 Z= 0.244 Chirality : 0.043 0.197 1284 Planarity : 0.003 0.032 1422 Dihedral : 9.343 90.143 1274 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 : 3.36 % Allowed : 26.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1044 helix: 1.61 (0.26), residues: 434 sheet: -0.40 (0.37), residues: 174 loop : -1.01 (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 0.009 0.001 PHE C 495 TYR 0.008 0.001 TYR D 732 ARG 0.009 0.001 ARG B 684 *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.971 Fit side-chains REVERT: B 453 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7187 (ttt-90) REVERT: B 637 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: B 675 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7355 (ptm-80) REVERT: B 761 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7648 (pttp) REVERT: C 418 ASN cc_start: 0.7826 (m-40) cc_final: 0.7605 (m110) REVERT: C 453 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5832 (ttm-80) REVERT: C 748 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8627 (mp) REVERT: D 454 ASP cc_start: 0.7575 (t0) cc_final: 0.7245 (t0) REVERT: D 669 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8144 (ttpt) REVERT: D 714 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6028 (pt0) REVERT: D 719 ASP cc_start: 0.8470 (p0) cc_final: 0.8240 (p0) outliers start: 30 outliers final: 16 residues processed: 142 average time/residue: 1.7146 time to fit residues: 255.1329 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 456 ASP 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 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 D residue 457 THR 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 742 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8538 Z= 0.266 Angle : 0.569 7.374 11520 Z= 0.281 Chirality : 0.046 0.220 1284 Planarity : 0.004 0.036 1422 Dihedral : 9.203 94.689 1269 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.25 % Allowed : 25.50 % Favored : 70.25 % 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: 1.35 (0.25), residues: 434 sheet: -0.42 (0.37), residues: 174 loop : -1.10 (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 C 412 PHE 0.015 0.002 PHE C 495 TYR 0.010 0.002 TYR B 421 ARG 0.009 0.001 ARG D 684 *********************** 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 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.066 Fit side-chains REVERT: A 634 GLU cc_start: 0.7266 (tp30) cc_final: 0.7062 (tp30) REVERT: A 699 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7267 (mmtt) REVERT: B 453 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7230 (ttt-90) REVERT: B 761 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7696 (pttp) REVERT: C 418 ASN cc_start: 0.7956 (m-40) cc_final: 0.7697 (m110) REVERT: C 453 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.5934 (ttm-80) REVERT: C 748 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 755 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8037 (mt-10) outliers start: 38 outliers final: 21 residues processed: 148 average time/residue: 1.6488 time to fit residues: 256.0548 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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 D residue 414 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8538 Z= 0.149 Angle : 0.499 7.252 11520 Z= 0.247 Chirality : 0.043 0.209 1284 Planarity : 0.004 0.042 1422 Dihedral : 8.134 91.229 1269 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.58 % Allowed : 26.17 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1044 helix: 1.58 (0.26), residues: 434 sheet: -0.45 (0.37), residues: 174 loop : -1.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.009 0.001 PHE A 495 TYR 0.009 0.001 TYR D 711 ARG 0.010 0.001 ARG B 684 *********************** 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 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.013 Fit side-chains REVERT: B 453 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7179 (ttt-90) REVERT: B 675 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7450 (ptm-80) REVERT: B 761 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (pttp) REVERT: C 418 ASN cc_start: 0.7874 (m-40) cc_final: 0.7621 (m110) REVERT: C 453 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5845 (ttm-80) REVERT: C 748 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 755 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: D 714 GLN cc_start: 0.6915 (mm-40) cc_final: 0.5874 (pt0) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 1.6636 time to fit residues: 240.9255 Evaluate side-chains 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 457 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8538 Z= 0.206 Angle : 0.533 7.185 11520 Z= 0.264 Chirality : 0.045 0.213 1284 Planarity : 0.004 0.049 1422 Dihedral : 7.906 92.541 1269 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.47 % Allowed : 26.40 % 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 (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: 1.48 (0.26), residues: 434 sheet: -0.46 (0.37), residues: 174 loop : -1.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.002 0.001 HIS D 412 PHE 0.012 0.001 PHE C 495 TYR 0.014 0.001 TYR A 673 ARG 0.011 0.001 ARG D 684 *********************** 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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.092 Fit side-chains REVERT: B 453 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7212 (ttt-90) REVERT: B 761 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7670 (pttp) REVERT: C 418 ASN cc_start: 0.7918 (m-40) cc_final: 0.7678 (m110) REVERT: C 453 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5880 (ttm-80) REVERT: C 748 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8686 (mp) REVERT: C 755 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8004 (mt-10) outliers start: 31 outliers final: 19 residues processed: 143 average time/residue: 1.6873 time to fit residues: 252.8615 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 474 ILE Chi-restraints excluded: chain B residue 721 MET 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 457 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8538 Z= 0.238 Angle : 0.555 7.050 11520 Z= 0.277 Chirality : 0.046 0.228 1284 Planarity : 0.004 0.051 1422 Dihedral : 7.784 94.265 1269 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.69 % Allowed : 26.06 % Favored : 70.25 % 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: 1.37 (0.25), residues: 434 sheet: -0.48 (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 C 495 TYR 0.009 0.001 TYR D 711 ARG 0.012 0.001 ARG D 684 *********************** 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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.053 Fit side-chains REVERT: B 453 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7212 (ttt-90) REVERT: B 675 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7621 (ptm-80) REVERT: B 761 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7689 (pttp) REVERT: C 418 ASN cc_start: 0.7964 (m-40) cc_final: 0.7712 (m110) REVERT: C 453 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5936 (ttm-80) REVERT: C 484 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8540 (m) REVERT: C 748 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 755 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8020 (mt-10) outliers start: 33 outliers final: 23 residues processed: 145 average time/residue: 1.6535 time to fit residues: 251.3885 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 651 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.0000 chunk 105 optimal weight: 0.5980 chunk 97 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7306 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.173 Angle : 0.513 6.719 11520 Z= 0.258 Chirality : 0.043 0.173 1284 Planarity : 0.004 0.055 1422 Dihedral : 7.393 92.774 1269 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.36 % Allowed : 26.51 % 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 (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: 1.52 (0.26), residues: 434 sheet: -0.48 (0.37), residues: 174 loop : -1.04 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE A 495 TYR 0.023 0.001 TYR A 673 ARG 0.013 0.001 ARG D 684 ********************** 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 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.018 Fit side-chains REVERT: A 407 MET cc_start: 0.8702 (mpp) cc_final: 0.8436 (mtt) REVERT: B 453 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7190 (ttt-90) REVERT: B 761 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7648 (pttp) REVERT: C 418 ASN cc_start: 0.7896 (m-40) cc_final: 0.7658 (m110) REVERT: C 453 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.5889 (ttm-80) REVERT: C 484 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8522 (m) REVERT: C 748 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 755 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 30 outliers final: 21 residues processed: 141 average time/residue: 1.6354 time to fit residues: 241.7075 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 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 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 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 4 optimal weight: 0.0770 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119023 restraints weight = 9736.446| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.15 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8538 Z= 0.125 Angle : 0.480 6.357 11520 Z= 0.242 Chirality : 0.042 0.125 1284 Planarity : 0.004 0.055 1422 Dihedral : 6.582 81.849 1269 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.80 % Allowed : 27.40 % 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 (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: 0.32 (0.26), residues: 1044 helix: 1.70 (0.26), residues: 434 sheet: -0.60 (0.38), residues: 166 loop : -0.95 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.003 0.001 HIS D 412 PHE 0.007 0.001 PHE B 495 TYR 0.008 0.001 TYR A 673 ARG 0.014 0.001 ARG B 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.16 seconds wall clock time: 76 minutes 52.05 seconds (4612.05 seconds total)