Starting phenix.real_space_refine on Fri Nov 15 04:04:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_29368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_29368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_29368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_29368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpl_29368/11_2024/8fpl_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-5513/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: 7.95, per 1000 atoms: 0.97 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: 2.60 Conformation dependent library (CDL) restraints added in 1.7 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: 0.94 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: 2.68 Time building geometry restraints manager: 2.86 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: 0.00 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.800 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.270 ------------------------------------------------------------------------------- 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 8344 Z= 1.120 Angle : 0.786 10.747 11272 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 *********************** 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 : 0.918 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: 1.4554 time to fit residues: 174.8739 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 : 1.089 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 8344 Z= 0.244 Angle : 0.516 6.740 11272 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 *********************** 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 : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7892 (ttpt) REVERT: B 643 THR cc_start: 0.8036 (p) cc_final: 0.7748 (t) REVERT: B 685 THR cc_start: 0.8203 (m) cc_final: 0.7709 (p) REVERT: B 695 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6937 (tmmt) REVERT: C 661 ARG cc_start: 0.7282 (ptp-110) cc_final: 0.7056 (ptp90) REVERT: C 662 SER cc_start: 0.7720 (t) cc_final: 0.7304 (p) REVERT: A 503 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8866 (ttm) REVERT: A 660 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6859 (ttp80) REVERT: A 705 GLU cc_start: 0.7775 (mp0) cc_final: 0.7371 (mp0) REVERT: D 458 LYS cc_start: 0.8256 (mppt) cc_final: 0.8003 (mppt) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 1.5499 time to fit residues: 223.2016 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 : 0.889 ------------------------------------------------------------------------------- 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 50 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8344 Z= 0.243 Angle : 0.509 7.105 11272 Z= 0.266 Chirality : 0.044 0.130 1240 Planarity : 0.003 0.045 1390 Dihedral : 11.484 103.389 1274 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.78 % Allowed : 19.37 % Favored : 77.84 % 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: 0.12 (0.26), residues: 1016 helix: 1.17 (0.25), residues: 456 sheet: -1.18 (0.41), residues: 140 loop : -0.59 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.004 0.001 HIS C 412 PHE 0.011 0.002 PHE A 438 TYR 0.015 0.001 TYR D 673 ARG 0.004 0.001 ARG D 453 *********************** 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: 24 poor density : 116 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7878 (ttpt) REVERT: B 685 THR cc_start: 0.8191 (m) cc_final: 0.7719 (p) REVERT: B 695 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7045 (tmmt) REVERT: C 503 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (ttm) REVERT: C 662 SER cc_start: 0.7709 (t) cc_final: 0.7293 (p) REVERT: A 503 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8907 (ttm) REVERT: A 660 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6881 (ttp80) REVERT: A 705 GLU cc_start: 0.7767 (mp0) cc_final: 0.7417 (mp0) REVERT: D 411 ASN cc_start: 0.7901 (p0) cc_final: 0.7646 (p0) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 1.5613 time to fit residues: 209.9103 Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 503 MET 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 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 447 ASP 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 68 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 overall best weight: 1.7364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8344 Z= 0.289 Angle : 0.550 8.670 11272 Z= 0.284 Chirality : 0.045 0.132 1240 Planarity : 0.004 0.046 1390 Dihedral : 11.404 101.958 1274 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.13 % Allowed : 19.49 % Favored : 77.38 % 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: -0.04 (0.26), residues: 1016 helix: 1.02 (0.25), residues: 456 sheet: -1.23 (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 A 412 PHE 0.013 0.002 PHE A 438 TYR 0.017 0.002 TYR D 673 ARG 0.004 0.001 ARG D 453 *********************** 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 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: B 685 THR cc_start: 0.8256 (m) cc_final: 0.7759 (p) REVERT: B 695 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7114 (tmmt) REVERT: B 705 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 503 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8880 (ttm) REVERT: C 662 SER cc_start: 0.7648 (t) cc_final: 0.7252 (p) REVERT: A 503 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8890 (ttm) REVERT: A 705 GLU cc_start: 0.7783 (mp0) cc_final: 0.7374 (mp0) REVERT: D 411 ASN cc_start: 0.7956 (p0) cc_final: 0.7721 (p0) REVERT: D 684 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7203 (ttm110) outliers start: 27 outliers final: 16 residues processed: 128 average time/residue: 1.4452 time to fit residues: 194.7732 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8344 Z= 0.281 Angle : 0.538 7.273 11272 Z= 0.278 Chirality : 0.045 0.130 1240 Planarity : 0.004 0.047 1390 Dihedral : 11.205 100.076 1274 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.36 % Allowed : 19.72 % Favored : 76.91 % 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: -0.05 (0.26), residues: 1016 helix: 1.04 (0.25), residues: 456 sheet: -1.23 (0.42), residues: 140 loop : -0.71 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.012 0.002 PHE A 438 TYR 0.018 0.002 TYR D 673 ARG 0.004 0.001 ARG D 453 *********************** 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 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: B 685 THR cc_start: 0.8234 (m) cc_final: 0.7756 (p) REVERT: B 695 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7116 (tmmt) REVERT: B 705 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: C 503 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (ttm) REVERT: C 662 SER cc_start: 0.7666 (t) cc_final: 0.7273 (p) REVERT: C 674 MET cc_start: 0.7373 (mtm) cc_final: 0.7164 (mtm) REVERT: A 503 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8889 (ttm) REVERT: A 705 GLU cc_start: 0.7782 (mp0) cc_final: 0.7349 (mp0) REVERT: D 684 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7188 (ttm110) REVERT: D 705 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (mp0) outliers start: 29 outliers final: 15 residues processed: 126 average time/residue: 1.5494 time to fit residues: 205.4003 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 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 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 Chi-restraints excluded: chain D residue 705 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8344 Z= 0.190 Angle : 0.491 8.769 11272 Z= 0.253 Chirality : 0.042 0.130 1240 Planarity : 0.003 0.047 1390 Dihedral : 10.740 98.206 1274 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.55 % Allowed : 20.65 % Favored : 76.80 % 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: 0.14 (0.26), residues: 1016 helix: 1.25 (0.25), residues: 456 sheet: -1.21 (0.41), residues: 140 loop : -0.65 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.002 0.001 HIS A 412 PHE 0.011 0.002 PHE D 658 TYR 0.016 0.001 TYR D 673 ARG 0.004 0.000 ARG D 453 *********************** 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 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: B 685 THR cc_start: 0.8082 (m) cc_final: 0.7631 (p) REVERT: B 695 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6837 (tmmt) REVERT: C 419 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 503 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8878 (ttm) REVERT: C 662 SER cc_start: 0.7634 (t) cc_final: 0.7289 (p) REVERT: A 503 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8884 (ttm) REVERT: A 705 GLU cc_start: 0.7763 (mp0) cc_final: 0.7410 (mp0) REVERT: D 454 ASP cc_start: 0.6721 (t0) cc_final: 0.6210 (t70) REVERT: D 684 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7121 (ttm110) outliers start: 22 outliers final: 13 residues processed: 121 average time/residue: 1.4725 time to fit residues: 187.6145 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 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 683 VAL Chi-restraints excluded: chain A residue 746 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 Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8344 Z= 0.159 Angle : 0.472 7.353 11272 Z= 0.243 Chirality : 0.042 0.132 1240 Planarity : 0.003 0.047 1390 Dihedral : 10.277 96.799 1274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.55 % Allowed : 20.65 % Favored : 76.80 % 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: 1.40 (0.25), residues: 456 sheet: -1.16 (0.41), residues: 140 loop : -0.59 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.003 0.001 HIS A 412 PHE 0.010 0.001 PHE D 658 TYR 0.015 0.001 TYR D 673 ARG 0.004 0.000 ARG B 453 *********************** 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 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.901 Fit side-chains REVERT: B 685 THR cc_start: 0.8026 (m) cc_final: 0.7586 (p) REVERT: B 695 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7002 (tmmt) REVERT: B 760 ASP cc_start: 0.8170 (m-30) cc_final: 0.7594 (m-30) REVERT: C 419 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 458 LYS cc_start: 0.7415 (mmtm) cc_final: 0.7198 (mmpt) REVERT: C 662 SER cc_start: 0.7553 (t) cc_final: 0.7219 (p) REVERT: A 503 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8839 (ttm) REVERT: D 454 ASP cc_start: 0.6749 (t0) cc_final: 0.6215 (t0) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 1.5178 time to fit residues: 200.4445 Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 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 746 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.003 0.043 8344 Z= 0.188 Angle : 0.504 9.334 11272 Z= 0.257 Chirality : 0.042 0.156 1240 Planarity : 0.003 0.047 1390 Dihedral : 10.216 95.906 1274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.67 % Allowed : 20.65 % 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: 0.29 (0.26), residues: 1016 helix: 1.39 (0.25), residues: 456 sheet: -1.12 (0.42), residues: 140 loop : -0.60 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.007 0.001 HIS C 412 PHE 0.010 0.002 PHE D 658 TYR 0.015 0.001 TYR D 673 ARG 0.004 0.000 ARG B 453 *********************** 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: 23 poor density : 105 time to evaluate : 1.016 Fit side-chains REVERT: B 434 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7921 (ttpt) REVERT: B 685 THR cc_start: 0.8042 (m) cc_final: 0.7594 (p) REVERT: B 695 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7051 (tmmt) REVERT: C 419 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 662 SER cc_start: 0.7546 (t) cc_final: 0.7230 (p) REVERT: A 503 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8860 (ttm) REVERT: D 454 ASP cc_start: 0.6793 (t0) cc_final: 0.6243 (t0) REVERT: D 684 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7121 (ttm110) outliers start: 23 outliers final: 15 residues processed: 118 average time/residue: 1.5311 time to fit residues: 189.7537 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 683 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8344 Z= 0.149 Angle : 0.475 7.663 11272 Z= 0.243 Chirality : 0.042 0.213 1240 Planarity : 0.003 0.047 1390 Dihedral : 9.662 93.964 1274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.20 % Allowed : 21.58 % Favored : 76.22 % 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: 0.40 (0.26), residues: 1016 helix: 1.53 (0.25), residues: 456 sheet: -1.11 (0.42), residues: 140 loop : -0.58 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.007 0.001 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 *********************** 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 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.977 Fit side-chains REVERT: B 434 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7935 (ttpt) REVERT: B 685 THR cc_start: 0.7910 (m) cc_final: 0.7443 (p) REVERT: B 695 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7004 (tmmt) REVERT: C 419 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 662 SER cc_start: 0.7461 (t) cc_final: 0.7172 (p) REVERT: A 503 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8830 (ttm) REVERT: D 454 ASP cc_start: 0.6788 (t0) cc_final: 0.6017 (t0) REVERT: D 684 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7096 (ttm110) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 1.4249 time to fit residues: 180.3891 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 683 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 746 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 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 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8344 Z= 0.191 Angle : 0.511 9.848 11272 Z= 0.260 Chirality : 0.043 0.207 1240 Planarity : 0.003 0.046 1390 Dihedral : 9.550 93.238 1274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.97 % Allowed : 21.69 % Favored : 76.33 % 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: 0.35 (0.26), residues: 1016 helix: 1.46 (0.25), residues: 456 sheet: -1.09 (0.42), residues: 140 loop : -0.58 (0.28), residues: 420 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 D 658 TYR 0.015 0.001 TYR D 673 ARG 0.005 0.000 ARG B 453 ********************** 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 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.955 Fit side-chains REVERT: B 434 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7919 (ttpt) REVERT: B 685 THR cc_start: 0.7991 (m) cc_final: 0.7501 (p) REVERT: B 695 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7048 (tmmt) REVERT: C 419 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 662 SER cc_start: 0.7546 (t) cc_final: 0.7228 (p) REVERT: A 503 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8866 (ttm) REVERT: D 454 ASP cc_start: 0.6806 (t0) cc_final: 0.6034 (t0) REVERT: D 684 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7122 (ttm110) REVERT: D 760 ASP cc_start: 0.8134 (m-30) cc_final: 0.7917 (m-30) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 1.4880 time to fit residues: 178.6913 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 : 1.025 ------------------------------------------------------------------------------- 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 683 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 746 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 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 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108612 restraints weight = 31832.754| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.27 r_work: 0.2947 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8344 Z= 0.145 Angle : 0.481 7.982 11272 Z= 0.246 Chirality : 0.042 0.186 1240 Planarity : 0.003 0.047 1390 Dihedral : 9.211 91.821 1274 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.86 % Allowed : 22.04 % Favored : 76.10 % 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: 0.45 (0.26), residues: 1016 helix: 1.56 (0.25), residues: 456 sheet: -1.05 (0.42), residues: 140 loop : -0.55 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.007 0.001 HIS C 412 PHE 0.010 0.001 PHE D 658 TYR 0.014 0.001 TYR D 673 ARG 0.005 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.07 seconds wall clock time: 64 minutes 58.22 seconds (3898.22 seconds total)