Starting phenix.real_space_refine on Sun May 11 16:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpl_29368/05_2025/8fpl_29368.cif" } resolution = 2.81 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= 0.004 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 5204 2.51 5 N 1354 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8178 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1998 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2012 Chain: "A" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1998 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2012 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS C 435 " occ=0.80 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.20 residue: pdb=" N AHIS D 435 " occ=0.80 ... (18 atoms not shown) pdb=" NE2BHIS D 435 " occ=0.20 Time building chain proxies: 7.89, per 1000 atoms: 0.96 Number of scatterers: 8178 At special positions: 0 Unit cell: (120.467, 99.1595, 73.755, 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 1552 8.00 N 1354 7.00 C 5204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 A 718 " - pdb=" SG CYS A 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: 2.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 19 sheets defined 44.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.001A 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 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 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 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 416 through 419 removed outlier: 3.989A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.584A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) 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 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 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 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 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 'D' and resid 416 through 419 removed outlier: 3.872A 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 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 489 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 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 'B' and resid 440 through 444 removed outlier: 6.477A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.804A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.521A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.656A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.669A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.467A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.623A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.623A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.608A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.842A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.588A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1011 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: 2.37 Time building geometry restraints manager: 2.48 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: 2550 1.35 - 1.48: 2055 1.48 - 1.60: 3595 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8344 Sorted by residual: bond pdb=" C3 CYZ D 902 " pdb=" C4 CYZ D 902 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C3 CYZ C 902 " pdb=" C4 CYZ C 902 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C3 CYZ A 902 " pdb=" C4 CYZ A 902 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B 902 " pdb=" C4 CYZ B 902 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C2 Y4Y D 901 " pdb=" O2 Y4Y D 901 " ideal model delta sigma weight residual 1.208 1.447 -0.239 2.00e-02 2.50e+03 1.43e+02 ... (remaining 8339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11041 2.15 - 4.30: 143 4.30 - 6.45: 55 6.45 - 8.60: 23 8.60 - 10.75: 10 Bond angle restraints: 11272 Sorted by residual: angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 123.45 -10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C9 CYZ A 902 " pdb=" S1 CYZ A 902 " pdb=" N1 CYZ A 902 " ideal model delta sigma weight residual 101.75 111.71 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C9 CYZ C 902 " pdb=" S1 CYZ C 902 " pdb=" N1 CYZ C 902 " ideal model delta sigma weight residual 101.75 111.61 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB MET A 408 " pdb=" CG MET A 408 " pdb=" SD MET A 408 " ideal model delta sigma weight residual 112.70 122.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ D 902 " pdb=" S1 CYZ D 902 " pdb=" N1 CYZ D 902 " ideal model delta sigma weight residual 101.75 111.56 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 11267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 4630 22.64 - 45.29: 381 45.29 - 67.93: 75 67.93 - 90.58: 15 90.58 - 113.22: 11 Dihedral angle restraints: 5112 sinusoidal: 2156 harmonic: 2956 Sorted by residual: dihedral pdb=" N2 CYZ A 902 " pdb=" C8 CYZ A 902 " pdb=" N1 CYZ A 902 " pdb=" S1 CYZ A 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.49 113.22 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" N2 CYZ C 902 " pdb=" C8 CYZ C 902 " pdb=" N1 CYZ C 902 " pdb=" S1 CYZ C 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.38 113.11 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" N2 CYZ D 902 " pdb=" C8 CYZ D 902 " pdb=" N1 CYZ D 902 " pdb=" S1 CYZ D 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.07 112.80 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1134 0.086 - 0.172: 90 0.172 - 0.258: 0 0.258 - 0.344: 0 0.344 - 0.430: 16 Chirality restraints: 1240 Sorted by residual: chirality pdb=" C8 CYZ A 902 " pdb=" C1 CYZ A 902 " pdb=" N1 CYZ A 902 " pdb=" N2 CYZ A 902 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C8 CYZ C 902 " pdb=" C1 CYZ C 902 " pdb=" N1 CYZ C 902 " pdb=" N2 CYZ C 902 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C8 CYZ B 902 " pdb=" C1 CYZ B 902 " pdb=" N1 CYZ B 902 " pdb=" N2 CYZ B 902 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1237 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO C 737 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 736 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 737 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 737 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 737 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 728 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" CG ASP A 728 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP A 728 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 728 " -0.007 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 326 2.72 - 3.27: 7833 3.27 - 3.81: 13785 3.81 - 4.36: 17480 4.36 - 4.90: 29098 Nonbonded interactions: 68522 Sorted by model distance: nonbonded pdb=" N GLU C 413 " pdb=" OE1 GLU C 413 " model vdw 2.177 3.120 nonbonded pdb=" N GLU A 413 " pdb=" OE1 GLU A 413 " model vdw 2.210 3.120 nonbonded pdb=" OG SER A 497 " pdb=" O2 CYZ A 902 " model vdw 2.252 3.040 nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C 902 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLU A 402 " pdb=" OH TYR A 450 " model vdw 2.288 3.040 ... (remaining 68517 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 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 763 or resid 765 through 773 or resid 901 through 902)) 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 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 763 or resid 765 through 773 or resid 901 through 902)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ ugh 773 or resid 901 through 902)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ ugh 773 or resid 901 through 902)) } 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=0.18 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.050 Find NCS groups from input model: 0.390 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.018 0.244 8348 Z= 0.884 Angle : 0.786 10.747 11280 Z= 0.328 Chirality : 0.062 0.430 1240 Planarity : 0.003 0.039 1390 Dihedral : 17.839 113.224 3220 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.35 % Allowed : 21.23 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: 0.21 (0.26), residues: 1016 helix: 1.31 (0.25), residues: 452 sheet: -1.06 (0.40), residues: 152 loop : -0.61 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.003 0.001 HIS A 412 PHE 0.008 0.002 PHE D 495 TYR 0.018 0.001 TYR A 647 ARG 0.007 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.16951 ( 351) hydrogen bonds : angle 6.19531 ( 1011) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.41844 ( 8) covalent geometry : bond 0.01773 ( 8344) covalent geometry : angle 0.78589 (11272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.869 Fit side-chains REVERT: B 685 THR cc_start: 0.8330 (m) cc_final: 0.7944 (p) REVERT: A 657 GLU cc_start: 0.7168 (mp0) cc_final: 0.6897 (mp0) outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 1.3868 time to fit residues: 166.6671 Evaluate side-chains 117 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 709 ASN D 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105694 restraints weight = 33766.554| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.54 r_work: 0.2896 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8348 Z= 0.155 Angle : 0.517 6.740 11280 Z= 0.271 Chirality : 0.044 0.133 1240 Planarity : 0.004 0.043 1390 Dihedral : 11.673 106.377 1274 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.44 % Allowed : 18.91 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: 1016 helix: 1.24 (0.25), residues: 456 sheet: -1.17 (0.41), residues: 140 loop : -0.48 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.005 0.002 HIS C 412 PHE 0.011 0.002 PHE A 438 TYR 0.014 0.002 TYR D 673 ARG 0.006 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 351) hydrogen bonds : angle 4.89894 ( 1011) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.92713 ( 8) covalent geometry : bond 0.00368 ( 8344) covalent geometry : angle 0.51647 (11272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: B 643 THR cc_start: 0.8084 (p) cc_final: 0.7829 (t) REVERT: B 685 THR cc_start: 0.8253 (m) cc_final: 0.7814 (p) REVERT: B 695 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7065 (tmmt) REVERT: C 661 ARG cc_start: 0.7146 (ptp-110) cc_final: 0.6935 (ptp90) REVERT: C 662 SER cc_start: 0.7894 (t) cc_final: 0.7428 (p) REVERT: A 503 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8896 (ttm) REVERT: A 660 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7043 (ttp80) REVERT: A 705 GLU cc_start: 0.8146 (mp0) cc_final: 0.7725 (mp0) REVERT: D 458 LYS cc_start: 0.8229 (mppt) cc_final: 0.7974 (mppt) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 1.3760 time to fit residues: 198.5382 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109877 restraints weight = 26464.287| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.72 r_work: 0.2998 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8348 Z= 0.091 Angle : 0.436 6.331 11280 Z= 0.229 Chirality : 0.041 0.125 1240 Planarity : 0.003 0.044 1390 Dihedral : 11.020 102.368 1274 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.09 % Allowed : 20.77 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1016 helix: 1.45 (0.26), residues: 456 sheet: -1.21 (0.41), residues: 140 loop : -0.47 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 766 HIS 0.003 0.001 HIS A 412 PHE 0.008 0.001 PHE D 658 TYR 0.012 0.001 TYR D 673 ARG 0.004 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 351) hydrogen bonds : angle 4.54221 ( 1011) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.28512 ( 8) covalent geometry : bond 0.00198 ( 8344) covalent geometry : angle 0.43560 (11272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.009 Fit side-chains REVERT: B 439 LYS cc_start: 0.8130 (mtmp) cc_final: 0.7739 (mmmm) REVERT: B 637 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: B 685 THR cc_start: 0.8029 (m) cc_final: 0.7629 (p) REVERT: B 695 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6971 (tmmt) REVERT: B 760 ASP cc_start: 0.8312 (m-30) cc_final: 0.7666 (m-30) REVERT: C 662 SER cc_start: 0.7766 (t) cc_final: 0.7354 (p) REVERT: A 660 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6959 (ttp80) REVERT: D 411 ASN cc_start: 0.7879 (p0) cc_final: 0.7645 (p0) REVERT: D 458 LYS cc_start: 0.8309 (mppt) cc_final: 0.8056 (mppt) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 1.3793 time to fit residues: 190.3073 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 709 ASN A 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104228 restraints weight = 26357.091| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.70 r_work: 0.2913 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.005 0.039 8348 Z= 0.212 Angle : 0.575 8.720 11280 Z= 0.294 Chirality : 0.046 0.133 1240 Planarity : 0.004 0.045 1390 Dihedral : 11.379 102.234 1274 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 19.37 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: -0.01 (0.26), residues: 1016 helix: 1.05 (0.25), residues: 456 sheet: -1.16 (0.42), residues: 140 loop : -0.67 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.015 0.003 PHE A 438 TYR 0.018 0.002 TYR D 673 ARG 0.004 0.001 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 351) hydrogen bonds : angle 4.78365 ( 1011) SS BOND : bond 0.00271 ( 4) SS BOND : angle 1.28900 ( 8) covalent geometry : bond 0.00514 ( 8344) covalent geometry : angle 0.57370 (11272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8023 (ttpt) REVERT: B 685 THR cc_start: 0.8287 (m) cc_final: 0.7866 (p) REVERT: B 695 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7215 (tmmt) REVERT: B 705 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: C 662 SER cc_start: 0.7808 (t) cc_final: 0.7351 (p) outliers start: 26 outliers final: 16 residues processed: 127 average time/residue: 1.4684 time to fit residues: 195.8332 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106688 restraints weight = 25464.949| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.46 r_work: 0.2972 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8348 Z= 0.119 Angle : 0.487 9.183 11280 Z= 0.249 Chirality : 0.042 0.128 1240 Planarity : 0.003 0.046 1390 Dihedral : 10.878 98.902 1274 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.32 % Allowed : 20.07 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: 1016 helix: 1.29 (0.25), residues: 456 sheet: -1.18 (0.42), residues: 140 loop : -0.64 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.002 0.001 HIS A 412 PHE 0.010 0.002 PHE D 658 TYR 0.015 0.001 TYR D 673 ARG 0.004 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 351) hydrogen bonds : angle 4.53863 ( 1011) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.50742 ( 8) covalent geometry : bond 0.00276 ( 8344) covalent geometry : angle 0.48711 (11272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 685 THR cc_start: 0.8115 (m) cc_final: 0.7737 (p) REVERT: B 695 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6925 (tmmt) REVERT: C 419 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7911 (mm-30) REVERT: C 662 SER cc_start: 0.7742 (t) cc_final: 0.7356 (p) REVERT: D 684 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7553 (ttm110) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 1.3839 time to fit residues: 186.5378 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 709 ASN A 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103141 restraints weight = 23336.531| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.93 r_work: 0.2943 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8348 Z= 0.216 Angle : 0.593 10.307 11280 Z= 0.300 Chirality : 0.046 0.135 1240 Planarity : 0.004 0.046 1390 Dihedral : 11.115 99.992 1274 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.67 % Allowed : 20.30 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: -0.11 (0.26), residues: 1016 helix: 0.99 (0.25), residues: 456 sheet: -1.18 (0.42), residues: 140 loop : -0.76 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 766 HIS 0.003 0.001 HIS D 412 PHE 0.015 0.003 PHE A 438 TYR 0.021 0.002 TYR D 673 ARG 0.004 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 351) hydrogen bonds : angle 4.75044 ( 1011) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.22770 ( 8) covalent geometry : bond 0.00524 ( 8344) covalent geometry : angle 0.59196 (11272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8068 (ttpt) REVERT: B 685 THR cc_start: 0.8253 (m) cc_final: 0.7859 (p) REVERT: B 695 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7265 (tmmt) REVERT: B 705 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 419 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7932 (mm-30) REVERT: C 662 SER cc_start: 0.7802 (t) cc_final: 0.7381 (p) REVERT: A 705 GLU cc_start: 0.7996 (mp0) cc_final: 0.7556 (mp0) REVERT: D 684 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7529 (ttm110) REVERT: D 705 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7886 (mp0) outliers start: 23 outliers final: 14 residues processed: 126 average time/residue: 1.4529 time to fit residues: 192.3774 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 705 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107767 restraints weight = 33022.893| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.80 r_work: 0.2915 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8348 Z= 0.102 Angle : 0.483 10.370 11280 Z= 0.245 Chirality : 0.042 0.127 1240 Planarity : 0.003 0.047 1390 Dihedral : 10.424 96.657 1274 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.09 % Allowed : 21.23 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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: 0.21 (0.26), residues: 1016 helix: 1.35 (0.25), residues: 456 sheet: -1.19 (0.41), residues: 140 loop : -0.66 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.002 0.001 HIS A 412 PHE 0.009 0.001 PHE D 658 TYR 0.014 0.001 TYR D 673 ARG 0.004 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 351) hydrogen bonds : angle 4.47169 ( 1011) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.32665 ( 8) covalent geometry : bond 0.00230 ( 8344) covalent geometry : angle 0.48291 (11272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: B 685 THR cc_start: 0.8075 (m) cc_final: 0.7683 (p) REVERT: B 695 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7007 (tmmt) REVERT: C 419 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 662 SER cc_start: 0.7754 (t) cc_final: 0.7365 (p) REVERT: A 503 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8864 (ttm) REVERT: D 684 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7607 (ttm110) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 1.3115 time to fit residues: 176.9873 Evaluate side-chains 121 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 709 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107778 restraints weight = 30459.225| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.23 r_work: 0.2943 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8348 Z= 0.106 Angle : 0.497 11.131 11280 Z= 0.248 Chirality : 0.042 0.147 1240 Planarity : 0.003 0.046 1390 Dihedral : 9.990 95.596 1274 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.32 % Allowed : 21.11 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1016 helix: 1.42 (0.25), residues: 456 sheet: -1.16 (0.41), residues: 140 loop : -0.62 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.007 0.002 HIS C 412 PHE 0.009 0.001 PHE D 658 TYR 0.013 0.001 TYR D 673 ARG 0.004 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 351) hydrogen bonds : angle 4.41267 ( 1011) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.48079 ( 8) covalent geometry : bond 0.00241 ( 8344) covalent geometry : angle 0.49674 (11272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: B 420 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6006 (ttp80) REVERT: B 434 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (ttpt) REVERT: B 685 THR cc_start: 0.8052 (m) cc_final: 0.7646 (p) REVERT: B 695 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7145 (tmmt) REVERT: B 760 ASP cc_start: 0.8373 (m-30) cc_final: 0.7772 (m-30) REVERT: C 419 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7817 (mm-30) REVERT: C 662 SER cc_start: 0.7710 (t) cc_final: 0.7362 (p) REVERT: A 503 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8844 (ttm) REVERT: D 684 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7576 (ttm110) outliers start: 20 outliers final: 12 residues processed: 119 average time/residue: 1.3620 time to fit residues: 171.2489 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104809 restraints weight = 33739.318| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.43 r_work: 0.2892 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8348 Z= 0.154 Angle : 0.564 12.740 11280 Z= 0.283 Chirality : 0.044 0.163 1240 Planarity : 0.004 0.046 1390 Dihedral : 10.154 95.707 1274 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.09 % Allowed : 21.46 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 (0.26), residues: 1016 helix: 1.27 (0.25), residues: 456 sheet: -1.35 (0.40), residues: 148 loop : -0.70 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.008 0.002 HIS C 412 PHE 0.011 0.002 PHE A 438 TYR 0.017 0.002 TYR D 673 ARG 0.005 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 351) hydrogen bonds : angle 4.54644 ( 1011) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.80713 ( 8) covalent geometry : bond 0.00367 ( 8344) covalent geometry : angle 0.56361 (11272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8061 (ttpt) REVERT: B 685 THR cc_start: 0.8131 (m) cc_final: 0.7734 (p) REVERT: B 695 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7274 (tmmt) REVERT: C 419 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 458 LYS cc_start: 0.7581 (mmpt) cc_final: 0.7373 (mmpt) REVERT: C 662 SER cc_start: 0.7718 (t) cc_final: 0.7357 (p) REVERT: A 503 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8894 (ttm) REVERT: D 454 ASP cc_start: 0.7031 (t0) cc_final: 0.6221 (t0) REVERT: D 684 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7608 (ttm110) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 1.2966 time to fit residues: 168.5988 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105225 restraints weight = 33938.046| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.55 r_work: 0.2885 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8348 Z= 0.151 Angle : 0.559 13.810 11280 Z= 0.280 Chirality : 0.044 0.204 1240 Planarity : 0.004 0.047 1390 Dihedral : 10.073 95.515 1274 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.09 % Allowed : 22.16 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 (0.26), residues: 1016 helix: 1.26 (0.25), residues: 456 sheet: -1.35 (0.41), residues: 148 loop : -0.69 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 766 HIS 0.008 0.002 HIS C 412 PHE 0.011 0.002 PHE A 438 TYR 0.017 0.001 TYR D 673 ARG 0.005 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 351) hydrogen bonds : angle 4.53863 ( 1011) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.76083 ( 8) covalent geometry : bond 0.00359 ( 8344) covalent geometry : angle 0.55861 (11272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: B 685 THR cc_start: 0.8123 (m) cc_final: 0.7716 (p) REVERT: B 695 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7238 (tmmt) REVERT: C 419 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 458 LYS cc_start: 0.7603 (mmpt) cc_final: 0.7370 (mmpt) REVERT: C 662 SER cc_start: 0.7805 (t) cc_final: 0.7421 (p) REVERT: A 503 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8923 (ttm) REVERT: D 454 ASP cc_start: 0.7004 (t0) cc_final: 0.6187 (t0) REVERT: D 684 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7653 (ttm110) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 1.3987 time to fit residues: 172.6541 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106648 restraints weight = 28841.598| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.05 r_work: 0.2938 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8348 Z= 0.115 Angle : 0.523 13.787 11280 Z= 0.263 Chirality : 0.043 0.211 1240 Planarity : 0.003 0.047 1390 Dihedral : 9.729 96.228 1274 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.97 % Allowed : 22.51 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1016 helix: 1.41 (0.25), residues: 456 sheet: -1.14 (0.42), residues: 140 loop : -0.61 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.007 0.002 HIS C 412 PHE 0.010 0.001 PHE D 658 TYR 0.015 0.001 TYR D 673 ARG 0.005 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 351) hydrogen bonds : angle 4.43995 ( 1011) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.42620 ( 8) covalent geometry : bond 0.00265 ( 8344) covalent geometry : angle 0.52311 (11272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5869.31 seconds wall clock time: 101 minutes 50.29 seconds (6110.29 seconds total)