Starting phenix.real_space_refine on Sat Jun 7 03:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq3_29376/06_2025/8fq3_29376.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8386 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.68 Number of scatterers: 8386 At special positions: 0 Unit cell: (122.031, 95.823, 82.719, 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 1602 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 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: 1.92 Conformation dependent library (CDL) restraints added in 919.3 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 18 sheets defined 44.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.677A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.558A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.840A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.547A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 705 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.577A pdb=" N LEU C 415 " --> pdb=" O HIS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.059A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' 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 489 removed outlier: 3.731A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.587A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.526A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) 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 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.669A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.527A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.845A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.501A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 705 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.565A pdb=" N LEU A 415 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.081A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' 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 489 removed outlier: 3.779A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.600A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 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 757 Processing helix chain 'A' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.014A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.144A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.752A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 490 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.222A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 395 through 399 removed outlier: 7.052A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.136A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.763A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 490 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.219A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 936 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: 2.32 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2041 1.48 - 1.60: 3723 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11313 2.03 - 4.07: 133 4.07 - 6.10: 39 6.10 - 8.13: 27 8.13 - 10.17: 8 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.92 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.86 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.61 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.57 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.22 9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.85: 4702 22.85 - 45.69: 455 45.69 - 68.54: 62 68.54 - 91.39: 19 91.39 - 114.24: 10 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 164.22 -71.22 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 162.93 -69.93 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual -86.00 -46.99 -39.01 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1196 0.088 - 0.175: 72 0.175 - 0.263: 0 0.263 - 0.350: 0 0.350 - 0.438: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C8 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" N2 CYZ B1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 767 " 0.014 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP A 767 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 767 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 767 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 767 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 767 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 767 " -0.013 2.00e-02 2.50e+03 1.05e-02 2.77e+00 pdb=" CG TRP C 767 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 767 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 767 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 767 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 767 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 767 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 767 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 625 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C THR D 625 " 0.026 2.00e-02 2.50e+03 pdb=" O THR D 625 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 626 " -0.008 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 422 2.73 - 3.27: 8012 3.27 - 3.81: 13977 3.81 - 4.36: 16661 4.36 - 4.90: 28393 Nonbonded interactions: 67465 Sorted by model distance: nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 497 " pdb=" O2 CYZ A1302 " model vdw 2.185 3.040 nonbonded pdb=" NH1 ARG B 715 " pdb=" O TRP B 767 " model vdw 2.248 3.120 nonbonded pdb=" NH1 ARG D 715 " pdb=" O TRP D 767 " model vdw 2.262 3.120 nonbonded pdb=" O VAL D 681 " pdb=" OH TYR D 700 " model vdw 2.270 3.040 ... (remaining 67460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.060 Set scattering table: 0.070 Process input model: 21.980 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.243 8542 Z= 0.724 Angle : 0.702 10.167 11528 Z= 0.297 Chirality : 0.061 0.438 1284 Planarity : 0.003 0.026 1422 Dihedral : 17.770 114.236 3288 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 23.15 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1044 helix: 1.22 (0.25), residues: 426 sheet: -0.93 (0.35), residues: 186 loop : -1.18 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 767 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE C 491 TYR 0.010 0.001 TYR C 424 ARG 0.002 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.18301 ( 314) hydrogen bonds : angle 6.86492 ( 936) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.45236 ( 8) covalent geometry : bond 0.01451 ( 8538) covalent geometry : angle 0.70196 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.890 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2425 time to fit residues: 38.5807 Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.195150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175096 restraints weight = 11579.803| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.03 r_work: 0.4035 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8542 Z= 0.144 Angle : 0.544 6.415 11528 Z= 0.269 Chirality : 0.043 0.176 1284 Planarity : 0.004 0.034 1422 Dihedral : 9.378 83.677 1266 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.80 % Allowed : 20.69 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1044 helix: 1.12 (0.25), residues: 430 sheet: -0.91 (0.35), residues: 186 loop : -1.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 767 HIS 0.002 0.001 HIS D 412 PHE 0.009 0.001 PHE D 659 TYR 0.019 0.002 TYR C 424 ARG 0.002 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 314) hydrogen bonds : angle 5.10035 ( 936) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.25485 ( 8) covalent geometry : bond 0.00346 ( 8538) covalent geometry : angle 0.54434 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.964 Fit side-chains REVERT: C 505 LYS cc_start: 0.5892 (mmtt) cc_final: 0.5372 (pptt) REVERT: C 647 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7043 (p90) REVERT: C 705 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: D 466 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: A 505 LYS cc_start: 0.6252 (mmtt) cc_final: 0.5548 (pptt) REVERT: A 647 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7000 (p90) REVERT: A 705 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6585 (mm-30) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.2247 time to fit residues: 43.5842 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.169615 restraints weight = 11766.534| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.07 r_work: 0.3952 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8542 Z= 0.206 Angle : 0.619 7.075 11528 Z= 0.309 Chirality : 0.047 0.242 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.153 67.022 1266 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.15 % Allowed : 21.25 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1044 helix: 0.65 (0.25), residues: 430 sheet: -1.04 (0.38), residues: 156 loop : -1.51 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 767 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.002 PHE D 495 TYR 0.026 0.002 TYR C 424 ARG 0.003 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 314) hydrogen bonds : angle 5.23536 ( 936) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.32846 ( 8) covalent geometry : bond 0.00498 ( 8538) covalent geometry : angle 0.61914 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.977 Fit side-chains REVERT: C 505 LYS cc_start: 0.6179 (mmtt) cc_final: 0.5575 (pptt) REVERT: C 647 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7531 (p90) REVERT: C 705 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: D 466 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 668 ASP cc_start: 0.6800 (t0) cc_final: 0.6499 (t0) REVERT: D 705 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: D 764 ASN cc_start: 0.8069 (m110) cc_final: 0.7842 (m110) REVERT: A 647 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7480 (p90) REVERT: A 705 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7070 (mm-30) outliers start: 46 outliers final: 32 residues processed: 153 average time/residue: 0.2197 time to fit residues: 45.8121 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.194645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175560 restraints weight = 11615.820| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.00 r_work: 0.4017 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.105 Angle : 0.481 6.170 11528 Z= 0.245 Chirality : 0.042 0.179 1284 Planarity : 0.003 0.039 1422 Dihedral : 6.631 55.703 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.69 % Allowed : 22.60 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1044 helix: 1.02 (0.26), residues: 430 sheet: -0.94 (0.35), residues: 186 loop : -1.27 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE D 659 TYR 0.010 0.001 TYR C 424 ARG 0.003 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 314) hydrogen bonds : angle 4.87158 ( 936) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.43304 ( 8) covalent geometry : bond 0.00248 ( 8538) covalent geometry : angle 0.48150 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.920 Fit side-chains REVERT: C 505 LYS cc_start: 0.6169 (mmtt) cc_final: 0.5560 (pptt) REVERT: C 642 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6115 (mp10) REVERT: C 647 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7376 (p90) REVERT: C 705 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: D 407 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6316 (mmm) REVERT: D 466 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: D 668 ASP cc_start: 0.6505 (t0) cc_final: 0.6280 (t0) REVERT: D 764 ASN cc_start: 0.8114 (m110) cc_final: 0.7898 (m110) REVERT: A 505 LYS cc_start: 0.6278 (mmtm) cc_final: 0.5767 (pptt) REVERT: A 637 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7272 (tp30) REVERT: A 647 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7276 (p90) REVERT: A 705 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: A 767 TRP cc_start: 0.6131 (m100) cc_final: 0.5736 (m100) outliers start: 33 outliers final: 23 residues processed: 156 average time/residue: 0.2164 time to fit residues: 45.5560 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.186172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166094 restraints weight = 11725.879| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.04 r_work: 0.3925 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 8542 Z= 0.260 Angle : 0.670 7.865 11528 Z= 0.339 Chirality : 0.049 0.222 1284 Planarity : 0.005 0.042 1422 Dihedral : 7.297 55.252 1266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.38 % Allowed : 20.81 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1044 helix: 0.49 (0.24), residues: 422 sheet: -1.28 (0.41), residues: 122 loop : -1.71 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.004 0.001 HIS D 412 PHE 0.013 0.002 PHE B 495 TYR 0.032 0.002 TYR A 424 ARG 0.004 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 314) hydrogen bonds : angle 5.32304 ( 936) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.17246 ( 8) covalent geometry : bond 0.00628 ( 8538) covalent geometry : angle 0.66913 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.881 Fit side-chains REVERT: B 407 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6600 (mmm) REVERT: B 705 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: C 505 LYS cc_start: 0.6416 (mmtt) cc_final: 0.5785 (pptt) REVERT: C 647 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7632 (p90) REVERT: C 705 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: D 407 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6518 (mmm) REVERT: D 466 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: D 628 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6516 (mmt-90) REVERT: D 668 ASP cc_start: 0.6909 (t0) cc_final: 0.6609 (t0) REVERT: D 705 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: D 764 ASN cc_start: 0.8170 (m110) cc_final: 0.7910 (m110) REVERT: A 637 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7342 (tp30) REVERT: A 647 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7633 (p90) REVERT: A 705 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7130 (mm-30) outliers start: 57 outliers final: 40 residues processed: 166 average time/residue: 0.2166 time to fit residues: 48.6249 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.173398 restraints weight = 11644.749| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.08 r_work: 0.4006 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8542 Z= 0.105 Angle : 0.490 6.980 11528 Z= 0.250 Chirality : 0.042 0.145 1284 Planarity : 0.004 0.055 1422 Dihedral : 6.247 48.473 1266 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.25 % Allowed : 22.71 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1044 helix: 0.90 (0.25), residues: 430 sheet: -1.04 (0.35), residues: 186 loop : -1.38 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.001 0.000 HIS D 412 PHE 0.007 0.001 PHE D 659 TYR 0.009 0.001 TYR A 424 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 314) hydrogen bonds : angle 4.79603 ( 936) SS BOND : bond 0.00450 ( 4) SS BOND : angle 0.99556 ( 8) covalent geometry : bond 0.00246 ( 8538) covalent geometry : angle 0.48942 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.881 Fit side-chains REVERT: B 459 ILE cc_start: 0.7572 (mm) cc_final: 0.7253 (mt) REVERT: B 473 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6149 (t0) REVERT: C 407 MET cc_start: 0.5212 (mpp) cc_final: 0.5010 (mpp) REVERT: C 505 LYS cc_start: 0.6202 (mmtt) cc_final: 0.5593 (pptt) REVERT: C 637 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7315 (tp30) REVERT: C 647 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7341 (p90) REVERT: C 705 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: C 767 TRP cc_start: 0.5943 (m100) cc_final: 0.5671 (m100) REVERT: C 773 CYS cc_start: 0.5727 (t) cc_final: 0.5490 (m) REVERT: D 407 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6191 (mmm) REVERT: D 466 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: D 628 ARG cc_start: 0.7273 (ttm170) cc_final: 0.6515 (mmt-90) REVERT: D 764 ASN cc_start: 0.8192 (m110) cc_final: 0.7930 (m110) REVERT: A 505 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.6065 (mmtm) REVERT: A 637 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7250 (tp30) REVERT: A 647 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7359 (p90) REVERT: A 705 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6647 (mm-30) outliers start: 38 outliers final: 27 residues processed: 156 average time/residue: 0.2164 time to fit residues: 45.4633 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 505 LYS Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.4980 chunk 17 optimal weight: 0.0010 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.196052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.177193 restraints weight = 11778.053| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.00 r_work: 0.4037 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8542 Z= 0.095 Angle : 0.469 5.327 11528 Z= 0.243 Chirality : 0.041 0.128 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.702 49.072 1266 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.91 % Allowed : 24.72 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1044 helix: 1.17 (0.26), residues: 430 sheet: -0.87 (0.36), residues: 186 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.001 0.000 HIS D 412 PHE 0.005 0.001 PHE D 659 TYR 0.008 0.001 TYR A 424 ARG 0.003 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02643 ( 314) hydrogen bonds : angle 4.65151 ( 936) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.92579 ( 8) covalent geometry : bond 0.00223 ( 8538) covalent geometry : angle 0.46854 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.930 Fit side-chains REVERT: B 407 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6491 (mmm) REVERT: B 459 ILE cc_start: 0.7440 (mm) cc_final: 0.7114 (mt) REVERT: C 505 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5639 (pptt) REVERT: C 637 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7255 (tp30) REVERT: C 647 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7140 (p90) REVERT: C 767 TRP cc_start: 0.5878 (m100) cc_final: 0.5414 (m100) REVERT: D 764 ASN cc_start: 0.8228 (m110) cc_final: 0.7953 (m110) REVERT: A 642 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6169 (mp10) REVERT: A 647 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7260 (p90) outliers start: 26 outliers final: 21 residues processed: 150 average time/residue: 0.2214 time to fit residues: 44.8732 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.191630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172376 restraints weight = 11783.259| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.02 r_work: 0.3994 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8542 Z= 0.135 Angle : 0.516 6.195 11528 Z= 0.265 Chirality : 0.042 0.128 1284 Planarity : 0.004 0.037 1422 Dihedral : 6.208 50.243 1266 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.91 % Allowed : 23.71 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1044 helix: 1.06 (0.25), residues: 430 sheet: -0.97 (0.36), residues: 186 loop : -1.40 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 767 HIS 0.002 0.001 HIS D 412 PHE 0.008 0.001 PHE D 659 TYR 0.016 0.001 TYR A 424 ARG 0.005 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 314) hydrogen bonds : angle 4.74815 ( 936) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.79260 ( 8) covalent geometry : bond 0.00326 ( 8538) covalent geometry : angle 0.51553 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.863 Fit side-chains REVERT: B 407 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6525 (mmm) REVERT: B 459 ILE cc_start: 0.7452 (mm) cc_final: 0.7147 (mt) REVERT: C 505 LYS cc_start: 0.6293 (mmtt) cc_final: 0.5676 (pptt) REVERT: C 647 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7359 (p90) REVERT: C 705 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: C 767 TRP cc_start: 0.6084 (m100) cc_final: 0.5655 (m100) REVERT: D 407 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6241 (mmm) REVERT: D 466 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: D 764 ASN cc_start: 0.8236 (m110) cc_final: 0.7953 (m110) REVERT: A 647 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7386 (p90) REVERT: A 705 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6831 (mm-30) outliers start: 35 outliers final: 28 residues processed: 149 average time/residue: 0.2290 time to fit residues: 45.9629 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.192051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173088 restraints weight = 11799.929| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.01 r_work: 0.4001 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8542 Z= 0.124 Angle : 0.506 5.815 11528 Z= 0.260 Chirality : 0.042 0.128 1284 Planarity : 0.004 0.036 1422 Dihedral : 6.160 50.447 1266 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.36 % Allowed : 23.27 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1044 helix: 1.09 (0.26), residues: 430 sheet: -0.94 (0.36), residues: 186 loop : -1.39 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 767 HIS 0.002 0.001 HIS D 412 PHE 0.007 0.001 PHE D 659 TYR 0.014 0.001 TYR C 424 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 314) hydrogen bonds : angle 4.69520 ( 936) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.63737 ( 8) covalent geometry : bond 0.00301 ( 8538) covalent geometry : angle 0.50544 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.883 Fit side-chains REVERT: B 407 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6523 (mmm) REVERT: C 505 LYS cc_start: 0.6335 (mmtt) cc_final: 0.5749 (pptt) REVERT: C 647 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7346 (p90) REVERT: C 705 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: D 407 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6201 (mmm) REVERT: D 466 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: D 764 ASN cc_start: 0.8227 (m110) cc_final: 0.7941 (m110) REVERT: A 647 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7465 (p90) REVERT: A 705 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6785 (mm-30) outliers start: 39 outliers final: 31 residues processed: 151 average time/residue: 0.2596 time to fit residues: 52.7027 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.187275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.168105 restraints weight = 11674.205| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.01 r_work: 0.3946 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8542 Z= 0.213 Angle : 0.613 7.270 11528 Z= 0.314 Chirality : 0.046 0.172 1284 Planarity : 0.004 0.045 1422 Dihedral : 6.874 51.706 1266 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.47 % Allowed : 23.38 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.25), residues: 1044 helix: 0.64 (0.25), residues: 432 sheet: -1.08 (0.40), residues: 146 loop : -1.48 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 767 HIS 0.004 0.001 HIS D 412 PHE 0.011 0.002 PHE B 495 TYR 0.027 0.002 TYR A 424 ARG 0.003 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 314) hydrogen bonds : angle 4.99216 ( 936) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.91463 ( 8) covalent geometry : bond 0.00516 ( 8538) covalent geometry : angle 0.61314 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.953 Fit side-chains REVERT: B 407 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.6642 (mmm) REVERT: B 628 ARG cc_start: 0.7355 (ttm170) cc_final: 0.6569 (mmt-90) REVERT: C 505 LYS cc_start: 0.6534 (mmtt) cc_final: 0.5884 (pptt) REVERT: C 647 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7477 (p90) REVERT: C 705 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: D 407 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6422 (mmm) REVERT: D 466 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: D 764 ASN cc_start: 0.8219 (m110) cc_final: 0.7928 (m110) REVERT: A 647 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7582 (p90) REVERT: A 705 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6950 (mm-30) outliers start: 40 outliers final: 32 residues processed: 149 average time/residue: 0.2182 time to fit residues: 44.0449 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.193738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174292 restraints weight = 11792.996| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.04 r_work: 0.4023 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8542 Z= 0.106 Angle : 0.492 5.323 11528 Z= 0.255 Chirality : 0.041 0.128 1284 Planarity : 0.004 0.038 1422 Dihedral : 6.096 50.038 1266 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.80 % Allowed : 23.94 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1044 helix: 1.03 (0.26), residues: 428 sheet: -0.95 (0.36), residues: 186 loop : -1.34 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 767 HIS 0.001 0.000 HIS A 412 PHE 0.006 0.001 PHE D 659 TYR 0.010 0.001 TYR A 647 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 314) hydrogen bonds : angle 4.68033 ( 936) SS BOND : bond 0.00102 ( 4) SS BOND : angle 1.14733 ( 8) covalent geometry : bond 0.00253 ( 8538) covalent geometry : angle 0.49162 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4906.21 seconds wall clock time: 85 minutes 58.27 seconds (5158.27 seconds total)