Starting phenix.real_space_refine on Fri Nov 15 06:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq3_29376/11_2024/8fq3_29376.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8386 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.79 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 18 sheets defined 44.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.677A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.558A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.840A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.547A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 705 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.577A pdb=" N LEU C 415 " --> pdb=" O HIS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.059A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.731A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.587A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.526A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.669A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.527A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.845A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.501A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 705 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.565A pdb=" N LEU A 415 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.081A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.779A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.600A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.014A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.747A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.144A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.752A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 490 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.143A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.222A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 395 through 399 removed outlier: 7.052A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.739A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.136A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.763A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 490 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.148A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.219A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.53 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.610 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- 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 8538 Z= 0.943 Angle : 0.702 10.167 11520 Z= 0.297 Chirality : 0.061 0.438 1284 Planarity : 0.003 0.026 1422 Dihedral : 17.770 114.236 3288 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 23.15 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1044 helix: 1.22 (0.25), residues: 426 sheet: -0.93 (0.35), residues: 186 loop : -1.18 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 767 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE C 491 TYR 0.010 0.001 TYR C 424 ARG 0.002 0.000 ARG C 661 *********************** 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 : 0.899 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2501 time to fit residues: 39.6074 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 : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8538 Z= 0.229 Angle : 0.544 6.415 11520 Z= 0.269 Chirality : 0.043 0.176 1284 Planarity : 0.004 0.034 1422 Dihedral : 9.378 83.677 1266 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.80 % Allowed : 20.69 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1044 helix: 1.12 (0.25), residues: 430 sheet: -0.91 (0.35), residues: 186 loop : -1.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 767 HIS 0.002 0.001 HIS D 412 PHE 0.009 0.001 PHE D 659 TYR 0.019 0.002 TYR C 424 ARG 0.002 0.000 ARG C 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.907 Fit side-chains REVERT: C 505 LYS cc_start: 0.5758 (mmtt) cc_final: 0.5376 (pptt) REVERT: C 647 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6862 (p90) REVERT: C 705 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: D 466 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: A 505 LYS cc_start: 0.6132 (mmtt) cc_final: 0.5538 (pptt) REVERT: A 647 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.6823 (p90) REVERT: A 705 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6553 (mm-30) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.2297 time to fit residues: 44.3747 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8538 Z= 0.299 Angle : 0.597 6.739 11520 Z= 0.298 Chirality : 0.046 0.236 1284 Planarity : 0.004 0.037 1422 Dihedral : 7.952 66.249 1266 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.03 % Allowed : 21.25 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1044 helix: 0.70 (0.25), residues: 432 sheet: -1.11 (0.36), residues: 176 loop : -1.35 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 767 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.002 PHE B 495 TYR 0.024 0.002 TYR A 424 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.129 Fit side-chains REVERT: C 505 LYS cc_start: 0.6018 (mmtt) cc_final: 0.5547 (pptt) REVERT: C 647 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7280 (p90) REVERT: C 673 TYR cc_start: 0.6443 (t80) cc_final: 0.6194 (t80) REVERT: C 705 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: D 466 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: D 705 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: A 505 LYS cc_start: 0.6385 (mmtt) cc_final: 0.5667 (pptt) REVERT: A 647 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7287 (p90) REVERT: A 705 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7039 (mm-30) outliers start: 45 outliers final: 31 residues processed: 153 average time/residue: 0.2261 time to fit residues: 46.7133 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 85 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8538 Z= 0.189 Angle : 0.498 6.149 11520 Z= 0.253 Chirality : 0.043 0.185 1284 Planarity : 0.003 0.037 1422 Dihedral : 6.714 56.037 1266 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.91 % Allowed : 22.60 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1044 helix: 0.97 (0.25), residues: 430 sheet: -0.96 (0.35), residues: 186 loop : -1.30 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 460 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE D 659 TYR 0.013 0.001 TYR C 424 ARG 0.003 0.000 ARG A 661 *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.993 Fit side-chains REVERT: C 505 LYS cc_start: 0.6008 (mmtt) cc_final: 0.5535 (pptt) REVERT: C 642 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6187 (mp10) REVERT: C 647 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7241 (p90) REVERT: C 705 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6634 (mm-30) REVERT: D 407 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6442 (mmm) REVERT: D 466 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: A 505 LYS cc_start: 0.5943 (mmtt) cc_final: 0.5481 (pptt) REVERT: A 647 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7239 (p90) REVERT: A 705 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6648 (mm-30) outliers start: 35 outliers final: 25 residues processed: 154 average time/residue: 0.2192 time to fit residues: 45.5090 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 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 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 chunk 42 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8538 Z= 0.393 Angle : 0.652 7.765 11520 Z= 0.331 Chirality : 0.049 0.222 1284 Planarity : 0.005 0.042 1422 Dihedral : 7.226 54.484 1266 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.15 % Allowed : 21.03 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1044 helix: 0.53 (0.25), residues: 422 sheet: -1.24 (0.41), residues: 122 loop : -1.71 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.004 0.001 HIS D 412 PHE 0.013 0.002 PHE B 495 TYR 0.030 0.002 TYR A 424 ARG 0.004 0.001 ARG A 661 *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.975 Fit side-chains REVERT: B 407 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.6844 (mmm) REVERT: B 705 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: C 505 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5734 (pptt) REVERT: C 647 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7480 (p90) REVERT: C 705 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: D 407 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6633 (mmm) REVERT: D 466 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: D 628 ARG cc_start: 0.6959 (ttm170) cc_final: 0.6405 (mmt-90) REVERT: D 705 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: A 505 LYS cc_start: 0.6223 (mmtt) cc_final: 0.5712 (pptt) REVERT: A 647 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7471 (p90) REVERT: A 705 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: A 767 TRP cc_start: 0.6217 (m100) cc_final: 0.5773 (m100) outliers start: 55 outliers final: 39 residues processed: 165 average time/residue: 0.2228 time to fit residues: 49.3906 Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8538 Z= 0.143 Angle : 0.470 6.617 11520 Z= 0.241 Chirality : 0.041 0.137 1284 Planarity : 0.004 0.054 1422 Dihedral : 6.058 48.846 1266 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.47 % Allowed : 23.94 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1044 helix: 0.98 (0.26), residues: 430 sheet: -0.97 (0.35), residues: 186 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.001 0.000 HIS D 412 PHE 0.009 0.001 PHE A 495 TYR 0.007 0.001 TYR A 647 ARG 0.004 0.000 ARG A 661 *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.985 Fit side-chains REVERT: B 459 ILE cc_start: 0.7586 (mm) cc_final: 0.7333 (mt) REVERT: C 407 MET cc_start: 0.5417 (mpp) cc_final: 0.5202 (mpp) REVERT: C 505 LYS cc_start: 0.6068 (mmtt) cc_final: 0.5610 (pptt) REVERT: C 642 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6218 (mp10) REVERT: C 647 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7159 (p90) REVERT: D 466 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: D 628 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6383 (mmt-90) REVERT: A 505 LYS cc_start: 0.6070 (mmtt) cc_final: 0.5596 (pptt) REVERT: A 647 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7187 (p90) outliers start: 31 outliers final: 24 residues processed: 152 average time/residue: 0.2236 time to fit residues: 45.8189 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 681 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 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 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 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 11 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8538 Z= 0.244 Angle : 0.538 6.580 11520 Z= 0.275 Chirality : 0.044 0.147 1284 Planarity : 0.004 0.043 1422 Dihedral : 6.489 49.900 1266 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.36 % Allowed : 23.94 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1044 helix: 0.89 (0.25), residues: 428 sheet: -1.08 (0.35), residues: 186 loop : -1.41 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.013 0.002 PHE D 438 TYR 0.018 0.002 TYR A 424 ARG 0.004 0.000 ARG A 661 *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.984 Fit side-chains REVERT: B 459 ILE cc_start: 0.7605 (mm) cc_final: 0.7354 (mt) REVERT: B 628 ARG cc_start: 0.6998 (ttm170) cc_final: 0.6452 (mmt-90) REVERT: C 505 LYS cc_start: 0.6059 (mmtt) cc_final: 0.5627 (pptt) REVERT: C 642 GLN cc_start: 0.7329 (tm-30) cc_final: 0.6236 (mp10) REVERT: C 647 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 705 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: D 407 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6404 (mmm) REVERT: D 466 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: D 628 ARG cc_start: 0.6953 (ttm170) cc_final: 0.6388 (mmt-90) REVERT: A 505 LYS cc_start: 0.6289 (mmtt) cc_final: 0.5718 (pptt) REVERT: A 647 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7252 (p90) REVERT: A 705 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: A 773 CYS cc_start: 0.5278 (t) cc_final: 0.5018 (m) outliers start: 39 outliers final: 33 residues processed: 150 average time/residue: 0.2285 time to fit residues: 46.2611 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 VAL 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 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 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 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 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8538 Z= 0.187 Angle : 0.492 5.797 11520 Z= 0.253 Chirality : 0.042 0.130 1284 Planarity : 0.004 0.038 1422 Dihedral : 6.185 50.004 1266 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.91 % Allowed : 24.16 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1044 helix: 0.99 (0.25), residues: 430 sheet: -1.02 (0.35), residues: 186 loop : -1.38 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.012 0.001 PHE D 438 TYR 0.013 0.001 TYR C 424 ARG 0.004 0.000 ARG A 661 *********************** 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.907 Fit side-chains REVERT: B 459 ILE cc_start: 0.7581 (mm) cc_final: 0.7326 (mt) REVERT: B 628 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6460 (mmt-90) REVERT: C 505 LYS cc_start: 0.6022 (mmtt) cc_final: 0.5563 (pptt) REVERT: C 642 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6215 (mp10) REVERT: C 647 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7272 (p90) REVERT: C 705 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: D 407 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.6310 (mmm) REVERT: D 466 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: A 505 LYS cc_start: 0.6202 (mmtt) cc_final: 0.5644 (pptt) REVERT: A 647 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7186 (p90) REVERT: A 705 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6617 (mm-30) outliers start: 35 outliers final: 27 residues processed: 144 average time/residue: 0.2310 time to fit residues: 44.7852 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 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 720 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8538 Z= 0.175 Angle : 0.487 5.779 11520 Z= 0.252 Chirality : 0.041 0.128 1284 Planarity : 0.004 0.037 1422 Dihedral : 6.023 50.528 1266 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.25 % Allowed : 23.94 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1044 helix: 1.10 (0.26), residues: 430 sheet: -0.96 (0.36), residues: 186 loop : -1.38 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 767 HIS 0.001 0.000 HIS D 412 PHE 0.009 0.001 PHE D 438 TYR 0.012 0.001 TYR C 424 ARG 0.004 0.000 ARG A 661 *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.921 Fit side-chains REVERT: C 505 LYS cc_start: 0.6092 (mmtt) cc_final: 0.5603 (pptt) REVERT: C 642 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6218 (mp10) REVERT: C 647 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7230 (p90) REVERT: C 705 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: D 407 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.6294 (mmm) REVERT: D 466 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: D 642 GLN cc_start: 0.7102 (pp30) cc_final: 0.6838 (tm-30) REVERT: A 642 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6248 (mp10) REVERT: A 647 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7190 (p90) REVERT: A 705 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6636 (mm-30) outliers start: 38 outliers final: 31 residues processed: 150 average time/residue: 0.2189 time to fit residues: 44.3788 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 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 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8538 Z= 0.193 Angle : 0.497 5.704 11520 Z= 0.256 Chirality : 0.042 0.127 1284 Planarity : 0.004 0.037 1422 Dihedral : 6.137 51.180 1266 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.59 % Allowed : 23.71 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1044 helix: 1.09 (0.26), residues: 430 sheet: -0.96 (0.36), residues: 186 loop : -1.37 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.009 0.001 PHE D 438 TYR 0.013 0.001 TYR C 424 ARG 0.002 0.000 ARG A 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.975 Fit side-chains REVERT: B 407 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.6694 (mmm) REVERT: B 628 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6492 (mmt-90) REVERT: C 642 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6219 (mp10) REVERT: C 647 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7142 (p90) REVERT: C 705 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: D 407 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6300 (mmm) REVERT: D 466 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: D 642 GLN cc_start: 0.7078 (pp30) cc_final: 0.6804 (tm-30) REVERT: A 642 GLN cc_start: 0.7338 (tm-30) cc_final: 0.6246 (mp10) REVERT: A 647 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7193 (p90) REVERT: A 705 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6660 (mm-30) outliers start: 41 outliers final: 34 residues processed: 146 average time/residue: 0.2255 time to fit residues: 44.5349 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 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 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.190731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171263 restraints weight = 11701.703| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.02 r_work: 0.3987 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8538 Z= 0.232 Angle : 0.529 6.389 11520 Z= 0.272 Chirality : 0.043 0.141 1284 Planarity : 0.004 0.040 1422 Dihedral : 6.432 51.343 1266 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.92 % Allowed : 23.27 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1044 helix: 0.99 (0.25), residues: 428 sheet: -1.01 (0.35), residues: 186 loop : -1.38 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 767 HIS 0.002 0.001 HIS D 412 PHE 0.012 0.002 PHE D 438 TYR 0.017 0.001 TYR A 424 ARG 0.002 0.000 ARG A 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.51 seconds wall clock time: 38 minutes 38.15 seconds (2318.15 seconds total)