Starting phenix.real_space_refine on Thu Jul 25 13:15:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t17_40956/07_2024/8t17_40956.cif" } resolution = 2.6 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= 0.048 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 56 5.16 5 C 9506 2.51 5 N 2688 2.21 5 O 2842 1.98 5 H 14462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 497": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29554 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "E" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "M" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "N" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Time building chain proxies: 13.48, per 1000 atoms: 0.46 Number of scatterers: 29554 At special positions: 0 Unit cell: (137.408, 133.951, 73.457, 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) S 56 16.00 O 2842 8.00 N 2688 7.00 C 9506 6.00 H 14462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 20.82 Conformation dependent library (CDL) restraints added in 3.1 seconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 14 sheets defined 35.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 408 through 428 removed outlier: 3.674A pdb=" N GLN A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU A 449 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU B 449 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 Processing helix chain 'D' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU D 449 " --> pdb=" O PRO D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU E 449 " --> pdb=" O PRO E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR E 462 " --> pdb=" O PHE E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 525 Processing helix chain 'F' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 449 removed outlier: 3.672A pdb=" N LEU F 449 " --> pdb=" O PRO F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 Processing helix chain 'G' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU G 449 " --> pdb=" O PRO G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 525 Processing helix chain 'H' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU H 413 " --> pdb=" O ALA H 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU H 449 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 525 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU I 413 " --> pdb=" O ALA I 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE I 414 " --> pdb=" O ARG I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS I 435 " --> pdb=" O GLU I 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE I 436 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU I 449 " --> pdb=" O PRO I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 525 Processing helix chain 'J' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU J 413 " --> pdb=" O ALA J 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU J 449 " --> pdb=" O PRO J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 525 Processing helix chain 'K' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE K 414 " --> pdb=" O ARG K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS K 435 " --> pdb=" O GLU K 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU K 449 " --> pdb=" O PRO K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR K 462 " --> pdb=" O PHE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 522 through 525 Processing helix chain 'L' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU L 413 " --> pdb=" O ALA L 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS L 435 " --> pdb=" O GLU L 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L 436 " --> pdb=" O ALA L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU L 449 " --> pdb=" O PRO L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 462 " --> pdb=" O PHE L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 525 Processing helix chain 'M' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 414 " --> pdb=" O ARG M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 449 removed outlier: 3.672A pdb=" N LEU M 449 " --> pdb=" O PRO M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE M 461 " --> pdb=" O ASP M 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR M 462 " --> pdb=" O PHE M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 525 Processing helix chain 'N' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU N 413 " --> pdb=" O ALA N 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 414 " --> pdb=" O ARG N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS N 435 " --> pdb=" O GLU N 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU N 449 " --> pdb=" O PRO N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE N 461 " --> pdb=" O ASP N 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR N 462 " --> pdb=" O PHE N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 522 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS A 530 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY A 440 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS A 532 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR A 442 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER A 534 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE A 444 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 518 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 531 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 516 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS A 533 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU A 514 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY A 535 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 512 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA A 490 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 485 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 492 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 483 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 494 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS B 530 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY B 440 " --> pdb=" O HIS B 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS B 532 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR B 442 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER B 534 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE B 444 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 518 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 531 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B 516 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS B 533 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU B 514 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 535 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 512 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA B 490 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL B 485 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 483 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 494 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS C 530 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY C 440 " --> pdb=" O HIS C 530 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N HIS C 532 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR C 442 " --> pdb=" O HIS C 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER C 534 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE C 444 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 518 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE C 531 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 516 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS C 533 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 514 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY C 535 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN C 512 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA C 490 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL C 485 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS C 492 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 483 " --> pdb=" O CYS C 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA C 494 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS D 530 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY D 440 " --> pdb=" O HIS D 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS D 532 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR D 442 " --> pdb=" O HIS D 532 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N SER D 534 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE D 444 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 518 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE D 531 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR D 516 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS D 533 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU D 514 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY D 535 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN D 512 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA D 490 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL D 485 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS D 492 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 483 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA D 494 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS E 530 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY E 440 " --> pdb=" O HIS E 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS E 532 " --> pdb=" O GLY E 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR E 442 " --> pdb=" O HIS E 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER E 534 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE E 444 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 518 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 531 " --> pdb=" O THR E 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 516 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS E 533 " --> pdb=" O GLU E 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 514 " --> pdb=" O CYS E 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY E 535 " --> pdb=" O GLN E 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN E 512 " --> pdb=" O GLY E 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA E 490 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL E 485 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS E 492 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL E 483 " --> pdb=" O CYS E 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA E 494 " --> pdb=" O PRO E 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS F 530 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY F 440 " --> pdb=" O HIS F 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS F 532 " --> pdb=" O GLY F 440 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR F 442 " --> pdb=" O HIS F 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER F 534 " --> pdb=" O THR F 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE F 444 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL F 518 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE F 531 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR F 516 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS F 533 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU F 514 " --> pdb=" O CYS F 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY F 535 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN F 512 " --> pdb=" O GLY F 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA F 490 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL F 485 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS F 492 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL F 483 " --> pdb=" O CYS F 492 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA F 494 " --> pdb=" O PRO F 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS G 530 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY G 440 " --> pdb=" O HIS G 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS G 532 " --> pdb=" O GLY G 440 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR G 442 " --> pdb=" O HIS G 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER G 534 " --> pdb=" O THR G 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE G 444 " --> pdb=" O SER G 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL G 518 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE G 531 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR G 516 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS G 533 " --> pdb=" O GLU G 514 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU G 514 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY G 535 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 512 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA G 490 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL G 485 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS G 492 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 483 " --> pdb=" O CYS G 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA G 494 " --> pdb=" O PRO G 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS H 530 " --> pdb=" O ASP H 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY H 440 " --> pdb=" O HIS H 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS H 532 " --> pdb=" O GLY H 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR H 442 " --> pdb=" O HIS H 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER H 534 " --> pdb=" O THR H 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE H 444 " --> pdb=" O SER H 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL H 518 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE H 531 " --> pdb=" O THR H 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 516 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS H 533 " --> pdb=" O GLU H 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU H 514 " --> pdb=" O CYS H 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY H 535 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN H 512 " --> pdb=" O GLY H 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA H 490 " --> pdb=" O VAL H 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL H 485 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA H 494 " --> pdb=" O PRO H 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS I 530 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY I 440 " --> pdb=" O HIS I 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS I 532 " --> pdb=" O GLY I 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR I 442 " --> pdb=" O HIS I 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER I 534 " --> pdb=" O THR I 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE I 444 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL I 518 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE I 531 " --> pdb=" O THR I 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR I 516 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS I 533 " --> pdb=" O GLU I 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU I 514 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY I 535 " --> pdb=" O GLN I 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN I 512 " --> pdb=" O GLY I 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA I 490 " --> pdb=" O VAL I 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL I 485 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS I 492 " --> pdb=" O VAL I 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL I 483 " --> pdb=" O CYS I 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA I 494 " --> pdb=" O PRO I 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS J 530 " --> pdb=" O ASP J 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY J 440 " --> pdb=" O HIS J 530 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N HIS J 532 " --> pdb=" O GLY J 440 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR J 442 " --> pdb=" O HIS J 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER J 534 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N PHE J 444 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL J 518 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE J 531 " --> pdb=" O THR J 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR J 516 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS J 533 " --> pdb=" O GLU J 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU J 514 " --> pdb=" O CYS J 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY J 535 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN J 512 " --> pdb=" O GLY J 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA J 490 " --> pdb=" O VAL J 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL J 485 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS J 492 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL J 483 " --> pdb=" O CYS J 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA J 494 " --> pdb=" O PRO J 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS K 530 " --> pdb=" O ASP K 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY K 440 " --> pdb=" O HIS K 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS K 532 " --> pdb=" O GLY K 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR K 442 " --> pdb=" O HIS K 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER K 534 " --> pdb=" O THR K 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE K 444 " --> pdb=" O SER K 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL K 518 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE K 531 " --> pdb=" O THR K 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR K 516 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS K 533 " --> pdb=" O GLU K 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU K 514 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY K 535 " --> pdb=" O GLN K 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN K 512 " --> pdb=" O GLY K 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA K 490 " --> pdb=" O VAL K 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL K 485 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS K 492 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL K 483 " --> pdb=" O CYS K 492 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA K 494 " --> pdb=" O PRO K 481 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS L 530 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY L 440 " --> pdb=" O HIS L 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS L 532 " --> pdb=" O GLY L 440 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR L 442 " --> pdb=" O HIS L 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER L 534 " --> pdb=" O THR L 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE L 444 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL L 518 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE L 531 " --> pdb=" O THR L 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR L 516 " --> pdb=" O PHE L 531 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS L 533 " --> pdb=" O GLU L 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU L 514 " --> pdb=" O CYS L 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 535 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN L 512 " --> pdb=" O GLY L 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA L 490 " --> pdb=" O VAL L 485 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL L 485 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS L 492 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL L 483 " --> pdb=" O CYS L 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA L 494 " --> pdb=" O PRO L 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS M 530 " --> pdb=" O ASP M 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY M 440 " --> pdb=" O HIS M 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS M 532 " --> pdb=" O GLY M 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR M 442 " --> pdb=" O HIS M 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER M 534 " --> pdb=" O THR M 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE M 444 " --> pdb=" O SER M 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL M 518 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE M 531 " --> pdb=" O THR M 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR M 516 " --> pdb=" O PHE M 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS M 533 " --> pdb=" O GLU M 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU M 514 " --> pdb=" O CYS M 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY M 535 " --> pdb=" O GLN M 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN M 512 " --> pdb=" O GLY M 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA M 490 " --> pdb=" O VAL M 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL M 485 " --> pdb=" O ALA M 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS M 492 " --> pdb=" O VAL M 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL M 483 " --> pdb=" O CYS M 492 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 494 " --> pdb=" O PRO M 481 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS N 530 " --> pdb=" O ASP N 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY N 440 " --> pdb=" O HIS N 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS N 532 " --> pdb=" O GLY N 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR N 442 " --> pdb=" O HIS N 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER N 534 " --> pdb=" O THR N 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE N 444 " --> pdb=" O SER N 534 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL N 518 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE N 531 " --> pdb=" O THR N 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR N 516 " --> pdb=" O PHE N 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS N 533 " --> pdb=" O GLU N 514 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU N 514 " --> pdb=" O CYS N 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY N 535 " --> pdb=" O GLN N 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN N 512 " --> pdb=" O GLY N 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA N 490 " --> pdb=" O VAL N 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL N 485 " --> pdb=" O ALA N 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS N 492 " --> pdb=" O VAL N 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL N 483 " --> pdb=" O CYS N 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA N 494 " --> pdb=" O PRO N 481 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1806 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: 10.98 Time building geometry restraints manager: 22.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 14420 1.12 - 1.30: 2615 1.30 - 1.47: 5262 1.47 - 1.64: 7579 1.64 - 1.81: 70 Bond restraints: 29946 Sorted by residual: bond pdb=" CE3 TRP B 519 " pdb=" HE3 TRP B 519 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE I 496 " pdb=" H ILE I 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE B 496 " pdb=" H ILE B 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 TYR C 495 " pdb=" HD2 TYR C 495 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE2 TYR B 495 " pdb=" HE2 TYR B 495 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 29941 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.12: 280 104.12 - 111.68: 30657 111.68 - 119.24: 11371 119.24 - 126.79: 11341 126.79 - 134.35: 321 Bond angle restraints: 53970 Sorted by residual: angle pdb=" CA HIS D 532 " pdb=" CB HIS D 532 " pdb=" CG HIS D 532 " ideal model delta sigma weight residual 113.80 119.62 -5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA HIS C 532 " pdb=" CB HIS C 532 " pdb=" CG HIS C 532 " ideal model delta sigma weight residual 113.80 119.61 -5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA HIS I 532 " pdb=" CB HIS I 532 " pdb=" CG HIS I 532 " ideal model delta sigma weight residual 113.80 119.60 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA HIS B 532 " pdb=" CB HIS B 532 " pdb=" CG HIS B 532 " ideal model delta sigma weight residual 113.80 119.60 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA HIS G 532 " pdb=" CB HIS G 532 " pdb=" CG HIS G 532 " ideal model delta sigma weight residual 113.80 119.59 -5.79 1.00e+00 1.00e+00 3.35e+01 ... (remaining 53965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 12768 13.64 - 27.28: 910 27.28 - 40.92: 294 40.92 - 54.56: 84 54.56 - 68.20: 168 Dihedral angle restraints: 14224 sinusoidal: 7658 harmonic: 6566 Sorted by residual: dihedral pdb=" CA SER F 443 " pdb=" C SER F 443 " pdb=" N PHE F 444 " pdb=" CA PHE F 444 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER J 443 " pdb=" C SER J 443 " pdb=" N PHE J 444 " pdb=" CA PHE J 444 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER G 443 " pdb=" C SER G 443 " pdb=" N PHE G 444 " pdb=" CA PHE G 444 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1019 0.050 - 0.101: 745 0.101 - 0.151: 280 0.151 - 0.202: 154 0.202 - 0.252: 42 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA GLU K 413 " pdb=" N GLU K 413 " pdb=" C GLU K 413 " pdb=" CB GLU K 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU D 413 " pdb=" N GLU D 413 " pdb=" C GLU D 413 " pdb=" CB GLU D 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU C 413 " pdb=" N GLU C 413 " pdb=" C GLU C 413 " pdb=" CB GLU C 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2237 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 517 " -0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG C 517 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 517 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 517 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 517 " 0.060 2.00e-02 2.50e+03 pdb="HH11 ARG C 517 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG C 517 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG C 517 " -0.119 2.00e-02 2.50e+03 pdb="HH22 ARG C 517 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 517 " -0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG D 517 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 517 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG D 517 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 517 " 0.059 2.00e-02 2.50e+03 pdb="HH11 ARG D 517 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG D 517 " -0.039 2.00e-02 2.50e+03 pdb="HH21 ARG D 517 " -0.119 2.00e-02 2.50e+03 pdb="HH22 ARG D 517 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 517 " 0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG I 517 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG I 517 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG I 517 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 517 " -0.059 2.00e-02 2.50e+03 pdb="HH11 ARG I 517 " 0.030 2.00e-02 2.50e+03 pdb="HH12 ARG I 517 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG I 517 " 0.119 2.00e-02 2.50e+03 pdb="HH22 ARG I 517 " -0.059 2.00e-02 2.50e+03 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2449 2.24 - 2.83: 52849 2.83 - 3.42: 76785 3.42 - 4.01: 102724 4.01 - 4.60: 151308 Nonbonded interactions: 386115 Sorted by model distance: nonbonded pdb=" HH TYR N 495 " pdb=" OE1 GLU N 515 " model vdw 1.649 1.850 nonbonded pdb=" HH TYR B 495 " pdb=" OE1 GLU B 515 " model vdw 1.649 1.850 nonbonded pdb=" HH TYR M 495 " pdb=" OE1 GLU M 515 " model vdw 1.649 1.850 nonbonded pdb=" HH TYR F 495 " pdb=" OE1 GLU F 515 " model vdw 1.649 1.850 nonbonded pdb=" HH TYR A 495 " pdb=" OE1 GLU A 515 " model vdw 1.649 1.850 ... (remaining 386110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 12.370 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: 3.440 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 86.660 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.160 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.013 0.037 15484 Z= 0.890 Angle : 1.884 5.980 21042 Z= 1.289 Chirality : 0.084 0.252 2240 Planarity : 0.011 0.057 2814 Dihedral : 12.069 68.202 5684 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1862 helix: -1.88 (0.16), residues: 476 sheet: 4.02 (0.19), residues: 574 loop : -1.21 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.010 TRP M 526 HIS 0.011 0.003 HIS L 520 PHE 0.027 0.011 PHE E 444 TYR 0.064 0.017 TYR E 462 ARG 0.005 0.001 ARG L 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.8406 (pt0) cc_final: 0.8141 (pt0) REVERT: A 460 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8208 (ttm-80) REVERT: B 460 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: B 509 ARG cc_start: 0.8257 (mmt180) cc_final: 0.8048 (mmp80) REVERT: C 454 GLU cc_start: 0.8705 (tt0) cc_final: 0.8443 (tt0) REVERT: C 456 MET cc_start: 0.8601 (mmm) cc_final: 0.8236 (mpp) REVERT: C 460 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7763 (ttp-110) REVERT: D 454 GLU cc_start: 0.8655 (tt0) cc_final: 0.8349 (tt0) REVERT: D 460 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8219 (ttm-80) REVERT: D 489 ASP cc_start: 0.8737 (m-30) cc_final: 0.8463 (p0) REVERT: D 509 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7970 (mmp80) REVERT: E 413 GLU cc_start: 0.8406 (pt0) cc_final: 0.8197 (pt0) REVERT: E 460 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8054 (ttt-90) REVERT: E 489 ASP cc_start: 0.8650 (m-30) cc_final: 0.8329 (p0) REVERT: F 460 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7645 (ttp-110) REVERT: G 413 GLU cc_start: 0.8417 (pt0) cc_final: 0.8160 (pt0) REVERT: G 423 GLU cc_start: 0.7809 (tp30) cc_final: 0.7511 (pt0) REVERT: G 454 GLU cc_start: 0.8690 (tt0) cc_final: 0.8343 (tt0) REVERT: G 460 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7379 (ttp-110) REVERT: G 489 ASP cc_start: 0.8716 (m-30) cc_final: 0.8493 (p0) REVERT: G 509 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7938 (mmp80) REVERT: H 413 GLU cc_start: 0.8470 (pt0) cc_final: 0.8200 (pt0) REVERT: H 460 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8164 (ttm-80) REVERT: I 460 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: J 454 GLU cc_start: 0.8709 (tt0) cc_final: 0.8471 (tt0) REVERT: J 456 MET cc_start: 0.8642 (mmm) cc_final: 0.8265 (mpp) REVERT: J 460 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7721 (ttp-110) REVERT: J 509 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7939 (mmp80) REVERT: K 413 GLU cc_start: 0.8328 (pt0) cc_final: 0.8074 (pt0) REVERT: K 454 GLU cc_start: 0.8680 (tt0) cc_final: 0.8322 (tt0) REVERT: K 460 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: K 489 ASP cc_start: 0.8751 (m-30) cc_final: 0.8460 (p0) REVERT: K 509 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7890 (mmp80) REVERT: L 460 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8044 (ttt-90) REVERT: L 489 ASP cc_start: 0.8690 (m-30) cc_final: 0.8376 (p0) REVERT: L 509 ARG cc_start: 0.8206 (mmt180) cc_final: 0.7992 (mmp80) REVERT: M 460 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7576 (ttp-110) REVERT: N 413 GLU cc_start: 0.8405 (pt0) cc_final: 0.8139 (pt0) REVERT: N 423 GLU cc_start: 0.7845 (tp30) cc_final: 0.7574 (pt0) REVERT: N 454 GLU cc_start: 0.8700 (tt0) cc_final: 0.8345 (tt0) REVERT: N 460 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7666 (ttp-110) REVERT: N 489 ASP cc_start: 0.8746 (m-30) cc_final: 0.8527 (p0) REVERT: N 509 ARG cc_start: 0.8232 (mmt180) cc_final: 0.8031 (mmp80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 3.0733 time to fit residues: 1444.4362 Evaluate side-chains 373 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN I 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15484 Z= 0.236 Angle : 0.684 5.475 21042 Z= 0.381 Chirality : 0.045 0.137 2240 Planarity : 0.006 0.053 2814 Dihedral : 5.722 19.629 2044 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.81 % Allowed : 7.45 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.20), residues: 1862 helix: -0.41 (0.21), residues: 476 sheet: 3.11 (0.22), residues: 616 loop : -0.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 519 HIS 0.004 0.001 HIS J 459 PHE 0.012 0.002 PHE E 444 TYR 0.010 0.002 TYR L 433 ARG 0.003 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 384 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 VAL cc_start: 0.8637 (t) cc_final: 0.7807 (m) REVERT: A 460 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: A 525 LYS cc_start: 0.7970 (tttp) cc_final: 0.7545 (ttpp) REVERT: B 460 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8070 (ttm-80) REVERT: B 509 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7855 (mmp80) REVERT: C 456 MET cc_start: 0.8485 (mmm) cc_final: 0.8131 (mpp) REVERT: C 460 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.7689 (ttp-110) REVERT: D 454 GLU cc_start: 0.8536 (tt0) cc_final: 0.8187 (tt0) REVERT: D 460 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8172 (ttm-80) REVERT: D 509 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7797 (mmp80) REVERT: E 460 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7995 (ttt-90) REVERT: G 413 GLU cc_start: 0.8041 (pt0) cc_final: 0.7819 (pt0) REVERT: G 423 GLU cc_start: 0.7888 (tp30) cc_final: 0.7495 (pt0) REVERT: G 454 GLU cc_start: 0.8566 (tt0) cc_final: 0.8261 (tt0) REVERT: G 456 MET cc_start: 0.8510 (mmm) cc_final: 0.8257 (mmm) REVERT: G 460 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7568 (ttp-110) REVERT: H 453 VAL cc_start: 0.8672 (t) cc_final: 0.7931 (m) REVERT: H 460 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: H 525 LYS cc_start: 0.7988 (tttp) cc_final: 0.7575 (ttpp) REVERT: I 460 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8055 (ttm-80) REVERT: J 454 GLU cc_start: 0.8587 (tt0) cc_final: 0.8336 (tt0) REVERT: J 456 MET cc_start: 0.8532 (mmm) cc_final: 0.8170 (mpp) REVERT: J 460 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7637 (ttp-110) REVERT: J 509 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7754 (mmp80) REVERT: K 454 GLU cc_start: 0.8559 (tt0) cc_final: 0.8205 (tt0) REVERT: K 460 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8236 (ttm-80) REVERT: K 509 ARG cc_start: 0.8001 (mmt180) cc_final: 0.7714 (mmp80) REVERT: L 460 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8002 (ttt-90) REVERT: M 454 GLU cc_start: 0.8375 (tt0) cc_final: 0.8128 (tt0) REVERT: M 460 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7589 (ttp-110) REVERT: N 413 GLU cc_start: 0.8077 (pt0) cc_final: 0.7843 (pt0) REVERT: N 423 GLU cc_start: 0.7880 (tp30) cc_final: 0.7516 (pt0) REVERT: N 454 GLU cc_start: 0.8569 (tt0) cc_final: 0.8250 (tt0) REVERT: N 456 MET cc_start: 0.8350 (mmm) cc_final: 0.8098 (mmm) REVERT: N 460 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7607 (ttp-110) outliers start: 13 outliers final: 2 residues processed: 386 average time/residue: 3.2089 time to fit residues: 1341.0543 Evaluate side-chains 379 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 377 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 528 ASN B 465 ASN C 465 ASN D 465 ASN D 528 ASN E 465 ASN F 465 ASN F 528 ASN G 465 ASN H 465 ASN H 500 GLN H 528 ASN I 465 ASN J 465 ASN K 465 ASN K 528 ASN L 465 ASN M 465 ASN M 528 ASN N 412 GLN N 465 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15484 Z= 0.232 Angle : 0.625 6.287 21042 Z= 0.345 Chirality : 0.046 0.151 2240 Planarity : 0.006 0.067 2814 Dihedral : 5.239 17.382 2044 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.43 % Allowed : 7.95 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.20), residues: 1862 helix: -0.19 (0.22), residues: 476 sheet: 3.25 (0.22), residues: 616 loop : -1.16 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 519 HIS 0.004 0.001 HIS J 459 PHE 0.014 0.002 PHE E 444 TYR 0.007 0.002 TYR N 495 ARG 0.004 0.001 ARG B 521 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 389 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 VAL cc_start: 0.8678 (t) cc_final: 0.7892 (m) REVERT: A 460 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8076 (ttm-80) REVERT: A 509 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7826 (mmm160) REVERT: A 525 LYS cc_start: 0.7941 (tttp) cc_final: 0.7505 (ttpp) REVERT: B 460 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: C 454 GLU cc_start: 0.8586 (tt0) cc_final: 0.8269 (tt0) REVERT: C 456 MET cc_start: 0.8358 (mmm) cc_final: 0.8031 (mpp) REVERT: C 460 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.7815 (ttp-110) REVERT: C 509 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7869 (mmp80) REVERT: D 454 GLU cc_start: 0.8532 (tt0) cc_final: 0.8204 (tt0) REVERT: D 460 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8189 (ttm-80) REVERT: D 509 ARG cc_start: 0.8036 (mmt180) cc_final: 0.7795 (mmm160) REVERT: E 453 VAL cc_start: 0.8646 (t) cc_final: 0.7952 (m) REVERT: E 460 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8028 (ttt-90) REVERT: E 509 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7356 (mmp80) REVERT: F 453 VAL cc_start: 0.8568 (t) cc_final: 0.7967 (m) REVERT: F 454 GLU cc_start: 0.8549 (tt0) cc_final: 0.8314 (tt0) REVERT: G 423 GLU cc_start: 0.7997 (tp30) cc_final: 0.7600 (pt0) REVERT: G 454 GLU cc_start: 0.8563 (tt0) cc_final: 0.8154 (tt0) REVERT: G 460 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: H 453 VAL cc_start: 0.8722 (t) cc_final: 0.8024 (m) REVERT: H 460 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8023 (ttm-80) REVERT: H 509 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (mmm160) REVERT: H 525 LYS cc_start: 0.7964 (tttp) cc_final: 0.7542 (ttpp) REVERT: I 460 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: J 454 GLU cc_start: 0.8601 (tt0) cc_final: 0.8318 (tt0) REVERT: J 456 MET cc_start: 0.8395 (mmm) cc_final: 0.8144 (mpp) REVERT: J 460 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7775 (ttp-110) REVERT: K 454 GLU cc_start: 0.8559 (tt0) cc_final: 0.8215 (tt0) REVERT: K 460 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8228 (ttm-80) REVERT: K 509 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7708 (mmm160) REVERT: L 453 VAL cc_start: 0.8566 (t) cc_final: 0.7855 (m) REVERT: L 460 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7980 (ttt-90) REVERT: M 454 GLU cc_start: 0.8424 (tt0) cc_final: 0.8200 (tt0) REVERT: N 423 GLU cc_start: 0.7977 (tp30) cc_final: 0.7616 (pt0) REVERT: N 454 GLU cc_start: 0.8557 (tt0) cc_final: 0.8141 (tt0) REVERT: N 460 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8009 (ttm-80) outliers start: 23 outliers final: 8 residues processed: 389 average time/residue: 3.1219 time to fit residues: 1318.0853 Evaluate side-chains 389 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 377 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 423 GLU Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN F 412 GLN K 412 GLN M 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15484 Z= 0.170 Angle : 0.549 5.089 21042 Z= 0.301 Chirality : 0.044 0.145 2240 Planarity : 0.006 0.075 2814 Dihedral : 4.990 17.950 2044 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.12 % Allowed : 8.57 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.20), residues: 1862 helix: 0.07 (0.22), residues: 476 sheet: 2.65 (0.22), residues: 686 loop : -0.58 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.003 0.001 HIS H 532 PHE 0.010 0.001 PHE L 444 TYR 0.005 0.001 TYR N 462 ARG 0.003 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 398 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 VAL cc_start: 0.8659 (t) cc_final: 0.7879 (m) REVERT: A 460 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: A 509 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7797 (mmm160) REVERT: A 525 LYS cc_start: 0.7860 (tttp) cc_final: 0.7453 (ttpp) REVERT: B 460 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8059 (ttm-80) REVERT: B 509 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7735 (mmm-85) REVERT: C 454 GLU cc_start: 0.8555 (tt0) cc_final: 0.8223 (tt0) REVERT: C 456 MET cc_start: 0.8284 (mmm) cc_final: 0.8025 (mpp) REVERT: C 460 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7826 (ttp-110) REVERT: C 509 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7813 (mmt90) REVERT: D 454 GLU cc_start: 0.8506 (tt0) cc_final: 0.8223 (tt0) REVERT: D 460 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8165 (ttm-80) REVERT: D 509 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7739 (mmm160) REVERT: E 453 VAL cc_start: 0.8625 (t) cc_final: 0.7944 (m) REVERT: E 460 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8038 (ttt-90) REVERT: E 509 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (mmm160) REVERT: F 454 GLU cc_start: 0.8508 (tt0) cc_final: 0.8295 (tt0) REVERT: F 460 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8081 (ttm-80) REVERT: G 423 GLU cc_start: 0.8063 (tp30) cc_final: 0.7653 (pt0) REVERT: G 454 GLU cc_start: 0.8530 (tt0) cc_final: 0.8223 (tt0) REVERT: G 460 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: H 453 VAL cc_start: 0.8702 (t) cc_final: 0.8009 (m) REVERT: H 460 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: H 509 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7794 (mmm160) REVERT: H 525 LYS cc_start: 0.7888 (tttp) cc_final: 0.7489 (ttpp) REVERT: I 460 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: J 454 GLU cc_start: 0.8564 (tt0) cc_final: 0.8265 (tt0) REVERT: J 456 MET cc_start: 0.8335 (mmm) cc_final: 0.8070 (mpp) REVERT: J 460 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.7784 (ttp-110) REVERT: J 509 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7670 (mmp80) REVERT: K 454 GLU cc_start: 0.8524 (tt0) cc_final: 0.8182 (tt0) REVERT: K 460 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8173 (ttm-80) REVERT: K 509 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7654 (mmm160) REVERT: L 453 VAL cc_start: 0.8540 (t) cc_final: 0.7838 (m) REVERT: L 460 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.7992 (ttt-90) REVERT: M 454 GLU cc_start: 0.8394 (tt0) cc_final: 0.8175 (tt0) REVERT: M 460 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: N 423 GLU cc_start: 0.8051 (tp30) cc_final: 0.7656 (pt0) REVERT: N 454 GLU cc_start: 0.8517 (tt0) cc_final: 0.8198 (tt0) REVERT: N 460 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8058 (ttm-80) outliers start: 18 outliers final: 11 residues processed: 398 average time/residue: 3.1437 time to fit residues: 1357.7014 Evaluate side-chains 418 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 403 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 423 GLU Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain K residue 489 ASP Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN D 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15484 Z= 0.278 Angle : 0.636 7.068 21042 Z= 0.350 Chirality : 0.047 0.153 2240 Planarity : 0.007 0.075 2814 Dihedral : 5.042 16.666 2044 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 8.88 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.20), residues: 1862 helix: -0.05 (0.22), residues: 476 sheet: 2.62 (0.22), residues: 686 loop : -0.76 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 519 HIS 0.004 0.001 HIS I 484 PHE 0.012 0.002 PHE L 444 TYR 0.007 0.002 TYR G 462 ARG 0.003 0.001 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 387 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: A 509 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (mmm160) REVERT: A 525 LYS cc_start: 0.7919 (tttp) cc_final: 0.7507 (ttpp) REVERT: B 423 GLU cc_start: 0.8268 (pt0) cc_final: 0.7736 (pt0) REVERT: B 460 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: C 454 GLU cc_start: 0.8596 (tt0) cc_final: 0.8258 (tt0) REVERT: C 456 MET cc_start: 0.8338 (mmm) cc_final: 0.8107 (mpp) REVERT: C 460 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7812 (ttp-110) REVERT: C 509 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7829 (mmp80) REVERT: D 454 GLU cc_start: 0.8568 (tt0) cc_final: 0.8264 (tt0) REVERT: D 460 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8145 (ttm-80) REVERT: D 509 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7738 (mmm160) REVERT: E 423 GLU cc_start: 0.8128 (pt0) cc_final: 0.7635 (pt0) REVERT: E 454 GLU cc_start: 0.8497 (tt0) cc_final: 0.8266 (tt0) REVERT: E 460 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8101 (ttt-90) REVERT: E 509 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7309 (mmp80) REVERT: F 454 GLU cc_start: 0.8552 (tt0) cc_final: 0.8298 (tt0) REVERT: F 460 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8096 (ttm-80) REVERT: G 423 GLU cc_start: 0.8028 (tp30) cc_final: 0.7680 (pt0) REVERT: G 454 GLU cc_start: 0.8563 (tt0) cc_final: 0.8164 (tt0) REVERT: G 460 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7994 (ttm-80) REVERT: H 460 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: H 525 LYS cc_start: 0.7948 (tttp) cc_final: 0.7546 (ttpp) REVERT: I 460 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8033 (ttm-80) REVERT: I 509 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7656 (mmp80) REVERT: J 454 GLU cc_start: 0.8604 (tt0) cc_final: 0.8375 (tt0) REVERT: J 456 MET cc_start: 0.8368 (mmm) cc_final: 0.8122 (mpp) REVERT: J 460 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.7769 (ttp-110) REVERT: K 454 GLU cc_start: 0.8580 (tt0) cc_final: 0.8263 (tt0) REVERT: K 460 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8153 (ttm-80) REVERT: K 509 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7664 (mmm160) REVERT: L 423 GLU cc_start: 0.8159 (pt0) cc_final: 0.7667 (pt0) REVERT: L 454 GLU cc_start: 0.8391 (tt0) cc_final: 0.8121 (tt0) REVERT: L 460 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8061 (ttt-90) REVERT: M 454 GLU cc_start: 0.8432 (tt0) cc_final: 0.8224 (tt0) REVERT: M 460 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8021 (ttm-80) REVERT: N 423 GLU cc_start: 0.8005 (tp30) cc_final: 0.7685 (pt0) REVERT: N 454 GLU cc_start: 0.8568 (tt0) cc_final: 0.8263 (tt0) REVERT: N 460 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8041 (ttm-80) outliers start: 19 outliers final: 8 residues processed: 387 average time/residue: 3.2618 time to fit residues: 1365.6186 Evaluate side-chains 393 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 381 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN I 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15484 Z= 0.229 Angle : 0.587 6.263 21042 Z= 0.324 Chirality : 0.045 0.150 2240 Planarity : 0.007 0.080 2814 Dihedral : 4.951 16.902 2044 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.18 % Allowed : 9.94 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.21), residues: 1862 helix: 0.02 (0.22), residues: 476 sheet: 2.63 (0.22), residues: 686 loop : -0.68 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 519 HIS 0.004 0.001 HIS I 484 PHE 0.010 0.002 PHE L 444 TYR 0.006 0.002 TYR L 462 ARG 0.003 0.001 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 391 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: A 525 LYS cc_start: 0.7919 (tttp) cc_final: 0.7525 (ttpp) REVERT: B 423 GLU cc_start: 0.8271 (pt0) cc_final: 0.7768 (pt0) REVERT: B 460 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8070 (ttm-80) REVERT: C 454 GLU cc_start: 0.8570 (tt0) cc_final: 0.8226 (tt0) REVERT: C 456 MET cc_start: 0.8295 (mmm) cc_final: 0.8046 (mpp) REVERT: C 460 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7826 (ttp-110) REVERT: C 509 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (mmp80) REVERT: D 454 GLU cc_start: 0.8549 (tt0) cc_final: 0.8236 (tt0) REVERT: D 460 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: D 509 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7769 (mmm160) REVERT: E 423 GLU cc_start: 0.8127 (pt0) cc_final: 0.7634 (pt0) REVERT: E 453 VAL cc_start: 0.8688 (t) cc_final: 0.8020 (m) REVERT: E 460 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: E 509 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7233 (mmp80) REVERT: F 423 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: F 454 GLU cc_start: 0.8547 (tt0) cc_final: 0.8287 (tt0) REVERT: F 460 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8102 (ttm-80) REVERT: G 423 GLU cc_start: 0.8055 (tp30) cc_final: 0.7710 (pt0) REVERT: G 454 GLU cc_start: 0.8547 (tt0) cc_final: 0.8145 (tt0) REVERT: G 460 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7980 (ttm-80) REVERT: H 460 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: H 525 LYS cc_start: 0.7951 (tttp) cc_final: 0.7558 (ttpp) REVERT: I 460 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8056 (ttm-80) REVERT: I 509 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7822 (mmm160) REVERT: J 454 GLU cc_start: 0.8573 (tt0) cc_final: 0.8258 (tt0) REVERT: J 456 MET cc_start: 0.8325 (mmm) cc_final: 0.8060 (mpp) REVERT: J 460 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7783 (ttp-110) REVERT: K 454 GLU cc_start: 0.8565 (tt0) cc_final: 0.8242 (tt0) REVERT: K 460 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8144 (ttm-80) REVERT: K 509 ARG cc_start: 0.7935 (mmt180) cc_final: 0.7629 (mmm160) REVERT: L 423 GLU cc_start: 0.8176 (pt0) cc_final: 0.7684 (pt0) REVERT: L 453 VAL cc_start: 0.8598 (t) cc_final: 0.7915 (m) REVERT: L 454 GLU cc_start: 0.8380 (tt0) cc_final: 0.8179 (tt0) REVERT: L 460 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8060 (ttt-90) REVERT: L 507 ARG cc_start: 0.7261 (mmp-170) cc_final: 0.6945 (mpp80) REVERT: M 423 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: M 454 GLU cc_start: 0.8429 (tt0) cc_final: 0.8214 (tt0) REVERT: M 460 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: N 423 GLU cc_start: 0.8035 (tp30) cc_final: 0.7718 (pt0) REVERT: N 454 GLU cc_start: 0.8554 (tt0) cc_final: 0.8145 (tt0) REVERT: N 460 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8028 (ttm-80) outliers start: 19 outliers final: 6 residues processed: 393 average time/residue: 3.1516 time to fit residues: 1346.5282 Evaluate side-chains 394 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 383 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN E 412 GLN L 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15484 Z= 0.206 Angle : 0.570 5.948 21042 Z= 0.314 Chirality : 0.045 0.153 2240 Planarity : 0.007 0.080 2814 Dihedral : 4.877 17.032 2044 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.93 % Allowed : 10.25 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.21), residues: 1862 helix: 0.12 (0.22), residues: 476 sheet: 2.60 (0.22), residues: 686 loop : -0.63 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.004 0.001 HIS B 484 PHE 0.012 0.002 PHE B 430 TYR 0.005 0.001 TYR N 462 ARG 0.003 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 388 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8092 (ttm-80) REVERT: A 525 LYS cc_start: 0.7916 (tttp) cc_final: 0.7511 (ttpp) REVERT: B 423 GLU cc_start: 0.8279 (pt0) cc_final: 0.7778 (pt0) REVERT: B 460 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: C 454 GLU cc_start: 0.8558 (tt0) cc_final: 0.8305 (tt0) REVERT: C 456 MET cc_start: 0.8285 (mmm) cc_final: 0.8021 (mpp) REVERT: C 460 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8103 (ttm-80) REVERT: C 509 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7842 (mmt90) REVERT: D 454 GLU cc_start: 0.8538 (tt0) cc_final: 0.8233 (tt0) REVERT: D 460 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: D 509 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7725 (mmm160) REVERT: D 521 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: E 423 GLU cc_start: 0.8110 (pt0) cc_final: 0.7654 (pt0) REVERT: E 453 VAL cc_start: 0.8680 (t) cc_final: 0.8019 (m) REVERT: E 460 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8090 (ttt-90) REVERT: F 423 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: F 454 GLU cc_start: 0.8543 (tt0) cc_final: 0.8283 (tt0) REVERT: F 460 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8108 (ttm-80) REVERT: G 423 GLU cc_start: 0.8004 (tp30) cc_final: 0.7718 (pt0) REVERT: G 454 GLU cc_start: 0.8535 (tt0) cc_final: 0.8135 (tt0) REVERT: G 460 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7971 (ttm-80) REVERT: H 460 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8018 (ttm-80) REVERT: H 525 LYS cc_start: 0.7942 (tttp) cc_final: 0.7543 (ttpp) REVERT: I 460 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: I 509 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7819 (mmm160) REVERT: J 454 GLU cc_start: 0.8565 (tt0) cc_final: 0.8245 (tt0) REVERT: J 460 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8062 (ttm-80) REVERT: K 454 GLU cc_start: 0.8559 (tt0) cc_final: 0.8241 (tt0) REVERT: K 460 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8164 (ttm-80) REVERT: K 509 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7645 (mmm160) REVERT: K 521 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: L 423 GLU cc_start: 0.8143 (pt0) cc_final: 0.7686 (pt0) REVERT: L 453 VAL cc_start: 0.8594 (t) cc_final: 0.7913 (m) REVERT: L 454 GLU cc_start: 0.8370 (tt0) cc_final: 0.8166 (tt0) REVERT: L 460 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8051 (ttt-90) REVERT: L 507 ARG cc_start: 0.7259 (mmp-170) cc_final: 0.6943 (mpp80) REVERT: M 423 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: M 454 GLU cc_start: 0.8428 (tt0) cc_final: 0.8159 (tt0) REVERT: M 460 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8061 (ttm-80) REVERT: N 423 GLU cc_start: 0.8044 (tp30) cc_final: 0.7705 (pt0) REVERT: N 454 GLU cc_start: 0.8535 (tt0) cc_final: 0.8131 (tt0) REVERT: N 460 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7981 (ttm-80) outliers start: 15 outliers final: 7 residues processed: 388 average time/residue: 3.1264 time to fit residues: 1317.0002 Evaluate side-chains 400 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 387 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 0.0030 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN L 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15484 Z= 0.174 Angle : 0.540 5.285 21042 Z= 0.296 Chirality : 0.044 0.144 2240 Planarity : 0.007 0.078 2814 Dihedral : 4.773 17.357 2044 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.12 % Allowed : 11.24 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.21), residues: 1862 helix: 0.28 (0.23), residues: 476 sheet: 2.60 (0.22), residues: 686 loop : -0.53 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.003 0.001 HIS B 484 PHE 0.013 0.001 PHE B 430 TYR 0.005 0.001 TYR N 462 ARG 0.009 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 400 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: A 525 LYS cc_start: 0.7908 (tttp) cc_final: 0.7497 (ttpp) REVERT: B 423 GLU cc_start: 0.8202 (pt0) cc_final: 0.7770 (pt0) REVERT: B 460 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: C 454 GLU cc_start: 0.8539 (tt0) cc_final: 0.8188 (tt0) REVERT: C 460 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: C 509 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7817 (mmt90) REVERT: D 423 GLU cc_start: 0.8281 (pt0) cc_final: 0.7782 (pt0) REVERT: D 454 GLU cc_start: 0.8520 (tt0) cc_final: 0.8208 (tt0) REVERT: D 460 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8134 (ttm-80) REVERT: D 521 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7995 (ttp80) REVERT: E 423 GLU cc_start: 0.8127 (pt0) cc_final: 0.7665 (pt0) REVERT: E 453 VAL cc_start: 0.8672 (t) cc_final: 0.8015 (m) REVERT: E 460 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8093 (ttt-90) REVERT: F 423 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: F 454 GLU cc_start: 0.8527 (tt0) cc_final: 0.8267 (tt0) REVERT: F 460 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8102 (ttm-80) REVERT: G 423 GLU cc_start: 0.7999 (tp30) cc_final: 0.7711 (pt0) REVERT: G 454 GLU cc_start: 0.8514 (tt0) cc_final: 0.8127 (tt0) REVERT: G 460 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8033 (ttm-80) REVERT: H 460 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8012 (ttm-80) REVERT: H 525 LYS cc_start: 0.7933 (tttp) cc_final: 0.7530 (ttpp) REVERT: I 460 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: I 509 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7808 (mmm160) REVERT: J 454 GLU cc_start: 0.8546 (tt0) cc_final: 0.8220 (tt0) REVERT: J 460 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: K 454 GLU cc_start: 0.8538 (tt0) cc_final: 0.8213 (tt0) REVERT: K 460 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8122 (ttm-80) REVERT: K 521 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: L 423 GLU cc_start: 0.8160 (pt0) cc_final: 0.7706 (pt0) REVERT: L 453 VAL cc_start: 0.8562 (t) cc_final: 0.7894 (m) REVERT: L 454 GLU cc_start: 0.8352 (tt0) cc_final: 0.8076 (tt0) REVERT: L 460 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8062 (ttt-90) REVERT: M 423 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: M 454 GLU cc_start: 0.8401 (tt0) cc_final: 0.8184 (tt0) REVERT: M 460 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8059 (ttm-80) REVERT: N 423 GLU cc_start: 0.7976 (tp30) cc_final: 0.7715 (pt0) REVERT: N 454 GLU cc_start: 0.8520 (tt0) cc_final: 0.8127 (tt0) REVERT: N 460 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8103 (ttm-80) outliers start: 18 outliers final: 5 residues processed: 402 average time/residue: 3.0810 time to fit residues: 1344.1284 Evaluate side-chains 409 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 398 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN L 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15484 Z= 0.158 Angle : 0.515 4.615 21042 Z= 0.279 Chirality : 0.044 0.140 2240 Planarity : 0.007 0.080 2814 Dihedral : 4.612 17.622 2044 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.81 % Allowed : 11.86 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.21), residues: 1862 helix: 0.47 (0.23), residues: 476 sheet: 2.59 (0.23), residues: 686 loop : -0.39 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 519 HIS 0.003 0.001 HIS M 520 PHE 0.009 0.001 PHE F 444 TYR 0.003 0.001 TYR N 462 ARG 0.008 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 398 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: A 525 LYS cc_start: 0.7861 (tttp) cc_final: 0.7455 (ttpp) REVERT: B 423 GLU cc_start: 0.8187 (pt0) cc_final: 0.7757 (pt0) REVERT: B 460 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: C 454 GLU cc_start: 0.8538 (tt0) cc_final: 0.8269 (tt0) REVERT: C 460 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: C 509 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7809 (mmt90) REVERT: D 423 GLU cc_start: 0.8259 (pt0) cc_final: 0.7922 (pt0) REVERT: D 454 GLU cc_start: 0.8504 (tt0) cc_final: 0.8187 (tt0) REVERT: D 460 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: D 521 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: E 423 GLU cc_start: 0.8120 (pt0) cc_final: 0.7667 (pt0) REVERT: E 453 VAL cc_start: 0.8639 (t) cc_final: 0.7983 (m) REVERT: E 460 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8099 (ttt-90) REVERT: F 423 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: F 454 GLU cc_start: 0.8513 (tt0) cc_final: 0.8294 (tt0) REVERT: F 460 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8189 (ttm-80) REVERT: G 423 GLU cc_start: 0.8003 (tp30) cc_final: 0.7706 (pt0) REVERT: G 454 GLU cc_start: 0.8488 (tt0) cc_final: 0.8202 (tt0) REVERT: G 460 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: H 460 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.8021 (ttm-80) REVERT: H 525 LYS cc_start: 0.7887 (tttp) cc_final: 0.7489 (ttpp) REVERT: I 460 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: J 454 GLU cc_start: 0.8525 (tt0) cc_final: 0.8279 (tt0) REVERT: J 460 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: K 454 GLU cc_start: 0.8522 (tt0) cc_final: 0.8192 (tt0) REVERT: K 460 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: K 521 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7881 (ttp80) REVERT: L 423 GLU cc_start: 0.8188 (pt0) cc_final: 0.7741 (pt0) REVERT: L 453 VAL cc_start: 0.8560 (t) cc_final: 0.7893 (m) REVERT: L 454 GLU cc_start: 0.8323 (tt0) cc_final: 0.8060 (tt0) REVERT: L 460 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8068 (ttt-90) REVERT: M 423 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: M 454 GLU cc_start: 0.8390 (tt0) cc_final: 0.8169 (tt0) REVERT: M 460 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: N 423 GLU cc_start: 0.7976 (tp30) cc_final: 0.7708 (pt0) REVERT: N 454 GLU cc_start: 0.8492 (tt0) cc_final: 0.8199 (tt0) REVERT: N 460 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8079 (ttm-80) outliers start: 13 outliers final: 5 residues processed: 398 average time/residue: 3.1799 time to fit residues: 1376.2860 Evaluate side-chains 405 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 395 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain N residue 489 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 111 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15484 Z= 0.143 Angle : 0.495 4.271 21042 Z= 0.266 Chirality : 0.043 0.141 2240 Planarity : 0.007 0.079 2814 Dihedral : 4.470 17.713 2044 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.43 % Allowed : 12.67 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.21), residues: 1862 helix: 0.69 (0.23), residues: 476 sheet: 2.57 (0.23), residues: 686 loop : -0.29 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 519 HIS 0.003 0.001 HIS M 520 PHE 0.009 0.001 PHE M 444 TYR 0.003 0.001 TYR H 462 ARG 0.007 0.000 ARG A 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 400 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8043 (ttm-80) REVERT: A 525 LYS cc_start: 0.7807 (tttp) cc_final: 0.7404 (ttpp) REVERT: B 423 GLU cc_start: 0.8168 (pt0) cc_final: 0.7736 (pt0) REVERT: B 460 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: B 485 VAL cc_start: 0.8189 (t) cc_final: 0.7928 (t) REVERT: C 454 GLU cc_start: 0.8515 (tt0) cc_final: 0.8155 (tt0) REVERT: C 460 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.7678 (ttp-110) REVERT: C 509 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7806 (mmt90) REVERT: D 423 GLU cc_start: 0.8247 (pt0) cc_final: 0.7904 (pt0) REVERT: D 454 GLU cc_start: 0.8487 (tt0) cc_final: 0.8166 (tt0) REVERT: D 460 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8116 (ttm-80) REVERT: D 521 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: E 423 GLU cc_start: 0.8080 (pt0) cc_final: 0.7625 (pt0) REVERT: E 453 VAL cc_start: 0.8629 (t) cc_final: 0.7975 (m) REVERT: E 460 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8068 (ttt-90) REVERT: E 509 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7808 (mmm160) REVERT: F 423 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: F 454 GLU cc_start: 0.8485 (tt0) cc_final: 0.8195 (tt0) REVERT: F 460 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: G 423 GLU cc_start: 0.7997 (tp30) cc_final: 0.7698 (pt0) REVERT: G 454 GLU cc_start: 0.8463 (tt0) cc_final: 0.8176 (tt0) REVERT: G 460 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: H 460 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8016 (ttm-80) REVERT: H 525 LYS cc_start: 0.7846 (tttp) cc_final: 0.7446 (ttpp) REVERT: I 456 MET cc_start: 0.8244 (mmm) cc_final: 0.8031 (mpp) REVERT: I 460 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8055 (ttm-80) REVERT: I 485 VAL cc_start: 0.8239 (t) cc_final: 0.8015 (t) REVERT: I 509 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7664 (mmm-85) REVERT: J 454 GLU cc_start: 0.8512 (tt0) cc_final: 0.8264 (tt0) REVERT: J 460 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.7616 (ttp-110) REVERT: K 454 GLU cc_start: 0.8501 (tt0) cc_final: 0.8169 (tt0) REVERT: K 460 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8161 (ttm-80) REVERT: K 521 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7858 (ttp80) REVERT: L 423 GLU cc_start: 0.8124 (pt0) cc_final: 0.7667 (pt0) REVERT: L 453 VAL cc_start: 0.8547 (t) cc_final: 0.7882 (m) REVERT: L 454 GLU cc_start: 0.8298 (tt0) cc_final: 0.8031 (tt0) REVERT: L 460 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8045 (ttt-90) REVERT: M 423 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: M 454 GLU cc_start: 0.8362 (tt0) cc_final: 0.8063 (tt0) REVERT: M 460 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: N 423 GLU cc_start: 0.7965 (tp30) cc_final: 0.7697 (pt0) REVERT: N 454 GLU cc_start: 0.8474 (tt0) cc_final: 0.8173 (tt0) REVERT: N 460 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8117 (ttm-80) outliers start: 7 outliers final: 0 residues processed: 400 average time/residue: 3.0960 time to fit residues: 1344.6947 Evaluate side-chains 403 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 398 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain M residue 423 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147641 restraints weight = 41390.278| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.61 r_work: 0.3600 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15484 Z= 0.151 Angle : 0.502 4.359 21042 Z= 0.269 Chirality : 0.043 0.144 2240 Planarity : 0.007 0.075 2814 Dihedral : 4.415 17.621 2044 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.56 % Allowed : 12.73 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.21), residues: 1862 helix: 0.73 (0.23), residues: 476 sheet: 2.56 (0.23), residues: 686 loop : -0.28 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 519 HIS 0.003 0.001 HIS B 484 PHE 0.010 0.001 PHE F 444 TYR 0.003 0.001 TYR H 462 ARG 0.007 0.000 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17743.74 seconds wall clock time: 305 minutes 5.30 seconds (18305.30 seconds total)