Starting phenix.real_space_refine on Fri Aug 22 22:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq3_29376/08_2025/8fq3_29376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq3_29376/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fq3_29376/08_2025/8fq3_29376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq3_29376/08_2025/8fq3_29376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fq3_29376/08_2025/8fq3_29376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq3_29376/08_2025/8fq3_29376.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.47, per 1000 atoms: 0.29 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: 0.69 Conformation dependent library (CDL) restraints added in 516.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.40 Time building geometry restraints manager: 0.94 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 4.210 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 : 8.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 661 TYR 0.010 0.001 TYR C 424 PHE 0.008 0.001 PHE C 491 TRP 0.029 0.001 TRP A 767 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.01451 ( 8538) covalent geometry : angle 0.70196 (11520) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.45236 ( 8) hydrogen bonds : bond 0.18301 ( 314) hydrogen bonds : angle 6.86492 ( 936) *********************** 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 : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1193 time to fit residues: 18.9420 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4630 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.202277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.182417 restraints weight = 11792.227| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.05 r_work: 0.4090 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.088 Angle : 0.467 6.565 11528 Z= 0.231 Chirality : 0.041 0.144 1284 Planarity : 0.003 0.033 1422 Dihedral : 9.415 86.308 1266 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.01 % Allowed : 21.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1044 helix: 1.44 (0.26), residues: 432 sheet: -0.73 (0.35), residues: 184 loop : -1.10 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 661 TYR 0.008 0.001 TYR C 424 PHE 0.006 0.001 PHE D 659 TRP 0.012 0.001 TRP A 767 HIS 0.001 0.000 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8538) covalent geometry : angle 0.46705 (11520) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.18845 ( 8) hydrogen bonds : bond 0.02835 ( 314) hydrogen bonds : angle 4.97623 ( 936) *********************** 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 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.348 Fit side-chains REVERT: C 505 LYS cc_start: 0.5824 (mmtt) cc_final: 0.5334 (pptt) REVERT: D 407 MET cc_start: 0.7875 (mmm) cc_final: 0.7564 (mtt) REVERT: A 505 LYS cc_start: 0.6105 (mmtt) cc_final: 0.5465 (pptt) outliers start: 18 outliers final: 10 residues processed: 138 average time/residue: 0.1130 time to fit residues: 20.8538 Evaluate side-chains 133 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 672 THR 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 626 VAL Chi-restraints excluded: chain D residue 681 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 100 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.191916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171550 restraints weight = 11611.606| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.08 r_work: 0.4000 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8542 Z= 0.174 Angle : 0.580 6.347 11528 Z= 0.289 Chirality : 0.045 0.242 1284 Planarity : 0.004 0.035 1422 Dihedral : 8.391 72.371 1266 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.58 % Allowed : 22.04 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1044 helix: 1.03 (0.25), residues: 430 sheet: -0.95 (0.35), residues: 186 loop : -1.29 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.023 0.002 TYR A 424 PHE 0.024 0.002 PHE C 491 TRP 0.010 0.001 TRP A 767 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8538) covalent geometry : angle 0.58060 (11520) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.34138 ( 8) hydrogen bonds : bond 0.04077 ( 314) hydrogen bonds : angle 5.05507 ( 936) *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: B 764 ASN cc_start: 0.8113 (m110) cc_final: 0.7898 (m110) REVERT: C 505 LYS cc_start: 0.6136 (mmtt) cc_final: 0.5506 (pptt) REVERT: C 647 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7260 (p90) REVERT: C 705 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: D 466 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 505 LYS cc_start: 0.6155 (mmtt) cc_final: 0.5528 (pptt) REVERT: A 647 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7246 (p90) REVERT: A 705 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7056 (mm-30) outliers start: 32 outliers final: 24 residues processed: 147 average time/residue: 0.1069 time to fit residues: 21.2614 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 666 VAL 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 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 481 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.191268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.171363 restraints weight = 11821.402| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.07 r_work: 0.3978 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8542 Z= 0.157 Angle : 0.537 6.138 11528 Z= 0.270 Chirality : 0.044 0.185 1284 Planarity : 0.004 0.038 1422 Dihedral : 7.055 60.037 1266 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.59 % Allowed : 22.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1044 helix: 0.89 (0.25), residues: 430 sheet: -1.01 (0.35), residues: 186 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.019 0.002 TYR C 424 PHE 0.021 0.002 PHE C 491 TRP 0.005 0.001 TRP C 767 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8538) covalent geometry : angle 0.53691 (11520) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.43123 ( 8) hydrogen bonds : bond 0.03682 ( 314) hydrogen bonds : angle 4.95638 ( 936) *********************** 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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.292 Fit side-chains REVERT: B 764 ASN cc_start: 0.8091 (m110) cc_final: 0.7854 (m110) REVERT: C 505 LYS cc_start: 0.6209 (mmtt) cc_final: 0.5585 (pptt) REVERT: C 647 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7424 (p90) REVERT: C 673 TYR cc_start: 0.6453 (t80) cc_final: 0.6198 (t80) REVERT: C 705 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: D 466 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: D 668 ASP cc_start: 0.6663 (t0) cc_final: 0.6372 (t0) REVERT: D 764 ASN cc_start: 0.8104 (m110) cc_final: 0.7882 (m110) REVERT: A 505 LYS cc_start: 0.6203 (mmtt) cc_final: 0.5571 (pptt) REVERT: A 647 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7439 (p90) REVERT: A 705 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7044 (mm-30) outliers start: 41 outliers final: 31 residues processed: 151 average time/residue: 0.1028 time to fit residues: 21.0932 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 82 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176167 restraints weight = 11690.799| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.00 r_work: 0.4042 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8542 Z= 0.099 Angle : 0.461 6.222 11528 Z= 0.235 Chirality : 0.041 0.140 1284 Planarity : 0.003 0.035 1422 Dihedral : 6.128 49.330 1266 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.80 % Allowed : 23.04 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1044 helix: 1.19 (0.26), residues: 430 sheet: -0.84 (0.36), residues: 186 loop : -1.26 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.010 0.001 TYR A 424 PHE 0.012 0.001 PHE C 491 TRP 0.005 0.001 TRP C 766 HIS 0.001 0.000 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8538) covalent geometry : angle 0.46054 (11520) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.79076 ( 8) hydrogen bonds : bond 0.02813 ( 314) hydrogen bonds : angle 4.74975 ( 936) *********************** 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 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.338 Fit side-chains REVERT: B 459 ILE cc_start: 0.7349 (mm) cc_final: 0.6980 (mt) REVERT: B 764 ASN cc_start: 0.8058 (m110) cc_final: 0.7807 (m110) REVERT: C 505 LYS cc_start: 0.6173 (mmtt) cc_final: 0.5571 (pptt) REVERT: C 637 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7254 (tp30) REVERT: C 642 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6113 (mp10) REVERT: C 647 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7388 (p90) REVERT: C 705 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: D 466 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: D 764 ASN cc_start: 0.8096 (m110) cc_final: 0.7872 (m110) REVERT: A 505 LYS cc_start: 0.6174 (mmtt) cc_final: 0.5565 (pptt) REVERT: A 647 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7269 (p90) REVERT: A 705 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6679 (mm-30) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 0.1052 time to fit residues: 21.7480 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 658 PHE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 708 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.195652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.176283 restraints weight = 11578.181| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.99 r_work: 0.4049 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8542 Z= 0.102 Angle : 0.465 6.206 11528 Z= 0.238 Chirality : 0.041 0.127 1284 Planarity : 0.003 0.034 1422 Dihedral : 5.888 49.686 1266 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.36 % Allowed : 22.71 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 1044 helix: 1.26 (0.26), residues: 430 sheet: -0.82 (0.36), residues: 186 loop : -1.26 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.011 0.001 TYR A 424 PHE 0.012 0.001 PHE A 491 TRP 0.005 0.001 TRP D 460 HIS 0.001 0.000 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8538) covalent geometry : angle 0.46419 (11520) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.98853 ( 8) hydrogen bonds : bond 0.02855 ( 314) hydrogen bonds : angle 4.68952 ( 936) *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.353 Fit side-chains REVERT: B 407 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6372 (mmm) REVERT: B 459 ILE cc_start: 0.7317 (mm) cc_final: 0.6959 (mt) REVERT: B 764 ASN cc_start: 0.8130 (m110) cc_final: 0.7851 (m110) REVERT: C 505 LYS cc_start: 0.6256 (mmtt) cc_final: 0.5639 (pptt) REVERT: C 637 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7234 (tp30) REVERT: C 642 GLN cc_start: 0.7384 (tm-30) cc_final: 0.6150 (mp10) REVERT: C 647 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7257 (p90) REVERT: C 705 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6660 (mm-30) REVERT: D 407 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7508 (mtt) REVERT: D 466 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: D 764 ASN cc_start: 0.8111 (m110) cc_final: 0.7850 (m110) REVERT: A 505 LYS cc_start: 0.6234 (mmtt) cc_final: 0.5615 (pptt) REVERT: A 647 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7274 (p90) REVERT: A 705 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6688 (mm-30) outliers start: 39 outliers final: 27 residues processed: 157 average time/residue: 0.1037 time to fit residues: 21.9234 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 708 MET 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 658 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.195108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175266 restraints weight = 11788.333| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.06 r_work: 0.4035 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.107 Angle : 0.473 6.206 11528 Z= 0.242 Chirality : 0.041 0.123 1284 Planarity : 0.003 0.033 1422 Dihedral : 5.893 50.462 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.25 % Allowed : 23.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1044 helix: 1.23 (0.26), residues: 430 sheet: -0.80 (0.36), residues: 186 loop : -1.25 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.012 0.001 TYR A 424 PHE 0.012 0.001 PHE C 491 TRP 0.005 0.001 TRP D 460 HIS 0.001 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8538) covalent geometry : angle 0.47254 (11520) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.63870 ( 8) hydrogen bonds : bond 0.02927 ( 314) hydrogen bonds : angle 4.70449 ( 936) *********************** 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 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.333 Fit side-chains REVERT: B 407 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6358 (mmm) REVERT: B 459 ILE cc_start: 0.7255 (mm) cc_final: 0.6892 (mt) REVERT: B 764 ASN cc_start: 0.8177 (m110) cc_final: 0.7867 (m110) REVERT: C 505 LYS cc_start: 0.6276 (mmtt) cc_final: 0.5617 (pptt) REVERT: C 637 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7211 (tp30) REVERT: C 642 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6138 (mp10) REVERT: C 647 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7270 (p90) REVERT: C 705 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: D 407 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: D 466 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 764 ASN cc_start: 0.8131 (m110) cc_final: 0.7851 (m110) REVERT: A 505 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5649 (pptt) REVERT: A 647 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7266 (p90) REVERT: A 705 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6709 (mm-30) outliers start: 38 outliers final: 29 residues processed: 153 average time/residue: 0.1044 time to fit residues: 21.6769 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 708 MET 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 658 PHE 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 708 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.192613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173037 restraints weight = 11601.343| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.02 r_work: 0.4003 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8542 Z= 0.135 Angle : 0.505 7.049 11528 Z= 0.258 Chirality : 0.043 0.137 1284 Planarity : 0.004 0.061 1422 Dihedral : 6.210 50.868 1266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.70 % Allowed : 23.27 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.26), residues: 1044 helix: 1.09 (0.25), residues: 430 sheet: -0.90 (0.36), residues: 186 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.016 0.001 TYR A 424 PHE 0.016 0.002 PHE A 491 TRP 0.018 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8538) covalent geometry : angle 0.50497 (11520) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.52895 ( 8) hydrogen bonds : bond 0.03329 ( 314) hydrogen bonds : angle 4.80228 ( 936) *********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.307 Fit side-chains REVERT: B 407 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6362 (mmm) REVERT: B 459 ILE cc_start: 0.7351 (mm) cc_final: 0.7008 (mt) REVERT: B 764 ASN cc_start: 0.8127 (m110) cc_final: 0.7822 (m110) REVERT: C 505 LYS cc_start: 0.6300 (mmtt) cc_final: 0.5659 (pptt) REVERT: C 637 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7262 (tp30) REVERT: C 642 GLN cc_start: 0.7376 (tm-30) cc_final: 0.6126 (mp10) REVERT: C 647 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7411 (p90) REVERT: C 705 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: D 407 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7532 (mtt) REVERT: D 466 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: D 764 ASN cc_start: 0.8097 (m110) cc_final: 0.7855 (m110) REVERT: A 505 LYS cc_start: 0.6310 (mmtt) cc_final: 0.5632 (pptt) REVERT: A 647 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7323 (p90) REVERT: A 705 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6972 (mm-30) outliers start: 42 outliers final: 32 residues processed: 153 average time/residue: 0.0901 time to fit residues: 18.8004 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 : 0.199 ------------------------------------------------------------------------------- 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 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 708 MET 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 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 658 PHE 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 708 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.190253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.170634 restraints weight = 11698.830| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.02 r_work: 0.3973 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8542 Z= 0.171 Angle : 0.553 6.947 11528 Z= 0.282 Chirality : 0.045 0.159 1284 Planarity : 0.004 0.051 1422 Dihedral : 6.591 50.739 1266 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.03 % Allowed : 22.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.25), residues: 1044 helix: 0.84 (0.25), residues: 430 sheet: -0.85 (0.39), residues: 156 loop : -1.44 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 661 TYR 0.021 0.002 TYR A 424 PHE 0.018 0.002 PHE C 491 TRP 0.015 0.001 TRP C 767 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8538) covalent geometry : angle 0.55279 (11520) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.62639 ( 8) hydrogen bonds : bond 0.03865 ( 314) hydrogen bonds : angle 4.94807 ( 936) *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.240 Fit side-chains REVERT: B 407 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6505 (mmm) REVERT: B 459 ILE cc_start: 0.7515 (mm) cc_final: 0.7146 (mt) REVERT: B 628 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6563 (mmt-90) REVERT: B 764 ASN cc_start: 0.8139 (m110) cc_final: 0.7828 (m110) REVERT: C 505 LYS cc_start: 0.6397 (mmtt) cc_final: 0.5804 (pptt) REVERT: C 637 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7313 (tp30) REVERT: C 642 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6140 (mp10) REVERT: C 647 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7469 (p90) REVERT: C 705 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: D 407 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.6414 (mmm) REVERT: D 466 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: D 628 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6567 (mmt-90) REVERT: D 764 ASN cc_start: 0.8153 (m110) cc_final: 0.7882 (m110) REVERT: A 505 LYS cc_start: 0.6405 (mmtt) cc_final: 0.5804 (pptt) REVERT: A 647 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7582 (p90) REVERT: A 705 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: A 713 GLU cc_start: 0.7576 (tt0) cc_final: 0.7363 (tt0) outliers start: 45 outliers final: 34 residues processed: 164 average time/residue: 0.0922 time to fit residues: 20.4781 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 693 VAL 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 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 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 508 GLN 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 708 MET 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 89 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.193477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174166 restraints weight = 11662.540| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.02 r_work: 0.4013 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8542 Z= 0.116 Angle : 0.501 5.586 11528 Z= 0.259 Chirality : 0.042 0.124 1284 Planarity : 0.004 0.039 1422 Dihedral : 6.121 50.727 1266 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.25 % Allowed : 23.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.26), residues: 1044 helix: 1.00 (0.25), residues: 430 sheet: -0.90 (0.36), residues: 186 loop : -1.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 661 TYR 0.012 0.001 TYR C 424 PHE 0.012 0.001 PHE A 491 TRP 0.011 0.001 TRP C 767 HIS 0.001 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8538) covalent geometry : angle 0.50039 (11520) SS BOND : bond 0.00112 ( 4) SS BOND : angle 1.05861 ( 8) hydrogen bonds : bond 0.03019 ( 314) hydrogen bonds : angle 4.78163 ( 936) ********************** 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 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.198 Fit side-chains REVERT: B 407 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.6404 (mmm) REVERT: B 459 ILE cc_start: 0.7357 (mm) cc_final: 0.7020 (mt) REVERT: B 764 ASN cc_start: 0.8102 (m110) cc_final: 0.7803 (m110) REVERT: C 505 LYS cc_start: 0.6049 (mmtt) cc_final: 0.5694 (pptt) REVERT: C 637 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7305 (tp30) REVERT: C 642 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6145 (mp10) REVERT: C 647 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7402 (p90) REVERT: C 705 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: D 407 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: D 466 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: D 764 ASN cc_start: 0.8180 (m110) cc_final: 0.7922 (m110) REVERT: A 505 LYS cc_start: 0.5999 (mmtt) cc_final: 0.5689 (pptt) REVERT: A 637 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7239 (tp30) REVERT: A 647 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7413 (p90) REVERT: A 705 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6719 (mm-30) outliers start: 38 outliers final: 29 residues processed: 154 average time/residue: 0.0880 time to fit residues: 18.2663 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 693 VAL Chi-restraints excluded: chain B residue 708 MET 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 693 VAL Chi-restraints excluded: chain D residue 708 MET 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 14 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.193378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173219 restraints weight = 11764.785| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.08 r_work: 0.4012 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8542 Z= 0.129 Angle : 0.516 6.057 11528 Z= 0.265 Chirality : 0.042 0.134 1284 Planarity : 0.004 0.041 1422 Dihedral : 6.164 51.371 1266 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.03 % Allowed : 23.49 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.26), residues: 1044 helix: 1.00 (0.25), residues: 430 sheet: -0.93 (0.36), residues: 186 loop : -1.40 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 684 TYR 0.015 0.001 TYR A 424 PHE 0.015 0.001 PHE C 491 TRP 0.012 0.001 TRP C 767 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8538) covalent geometry : angle 0.51516 (11520) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.19614 ( 8) hydrogen bonds : bond 0.03249 ( 314) hydrogen bonds : angle 4.80053 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.76 seconds wall clock time: 41 minutes 14.03 seconds (2474.03 seconds total)