Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 21 00:58:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/10_2023/8p2m_17370.pdb" } resolution = 3.82 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= 0.003 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 307 5.16 5 C 29840 2.51 5 N 7918 2.21 5 O 8637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 821": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B ARG 774": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 613": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 683": "NH1" <-> "NH2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ARG 774": "NH1" <-> "NH2" Residue "C ARG 821": "NH1" <-> "NH2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 613": "NH1" <-> "NH2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 683": "NH1" <-> "NH2" Residue "D ARG 715": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D ARG 736": "NH1" <-> "NH2" Residue "D ARG 774": "NH1" <-> "NH2" Residue "D ARG 821": "NH1" <-> "NH2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 477": "NH1" <-> "NH2" Residue "E ARG 486": "NH1" <-> "NH2" Residue "E ARG 487": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "E ARG 491": "NH1" <-> "NH2" Residue "E ARG 611": "NH1" <-> "NH2" Residue "E ARG 613": "NH1" <-> "NH2" Residue "E ARG 616": "NH1" <-> "NH2" Residue "E ARG 660": "NH1" <-> "NH2" Residue "E ARG 683": "NH1" <-> "NH2" Residue "E ARG 715": "NH1" <-> "NH2" Residue "E ARG 716": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 736": "NH1" <-> "NH2" Residue "E ARG 774": "NH1" <-> "NH2" Residue "E ARG 821": "NH1" <-> "NH2" Residue "E ARG 845": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ASP 356": "OD1" <-> "OD2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 439": "NH1" <-> "NH2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 477": "NH1" <-> "NH2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F ARG 488": "NH1" <-> "NH2" Residue "F ARG 491": "NH1" <-> "NH2" Residue "F ARG 611": "NH1" <-> "NH2" Residue "F ARG 613": "NH1" <-> "NH2" Residue "F ARG 616": "NH1" <-> "NH2" Residue "F ARG 660": "NH1" <-> "NH2" Residue "F ARG 683": "NH1" <-> "NH2" Residue "F ARG 715": "NH1" <-> "NH2" Residue "F ARG 716": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 736": "NH1" <-> "NH2" Residue "F ARG 774": "NH1" <-> "NH2" Residue "F GLU 813": "OE1" <-> "OE2" Residue "F ARG 821": "NH1" <-> "NH2" Residue "F ARG 845": "NH1" <-> "NH2" Residue "G ARG 240": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G ARG 376": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ARG 439": "NH1" <-> "NH2" Residue "G ARG 461": "NH1" <-> "NH2" Residue "G ARG 477": "NH1" <-> "NH2" Residue "G ARG 486": "NH1" <-> "NH2" Residue "G ARG 487": "NH1" <-> "NH2" Residue "G ARG 488": "NH1" <-> "NH2" Residue "G ARG 491": "NH1" <-> "NH2" Residue "G ARG 611": "NH1" <-> "NH2" Residue "G ARG 613": "NH1" <-> "NH2" Residue "G ARG 616": "NH1" <-> "NH2" Residue "G ARG 660": "NH1" <-> "NH2" Residue "G ARG 683": "NH1" <-> "NH2" Residue "G ARG 715": "NH1" <-> "NH2" Residue "G ARG 716": "NH1" <-> "NH2" Residue "G ARG 733": "NH1" <-> "NH2" Residue "G ARG 736": "NH1" <-> "NH2" Residue "G ARG 774": "NH1" <-> "NH2" Residue "G ARG 821": "NH1" <-> "NH2" Residue "G ARG 845": "NH1" <-> "NH2" Residue "H ARG 240": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 332": "NH1" <-> "NH2" Residue "H ARG 367": "NH1" <-> "NH2" Residue "H ARG 376": "NH1" <-> "NH2" Residue "H ARG 418": "NH1" <-> "NH2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "H ARG 461": "NH1" <-> "NH2" Residue "H ARG 477": "NH1" <-> "NH2" Residue "H ARG 486": "NH1" <-> "NH2" Residue "H ARG 487": "NH1" <-> "NH2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "H ARG 491": "NH1" <-> "NH2" Residue "H ARG 611": "NH1" <-> "NH2" Residue "H ARG 613": "NH1" <-> "NH2" Residue "H ARG 616": "NH1" <-> "NH2" Residue "H ARG 660": "NH1" <-> "NH2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ARG 715": "NH1" <-> "NH2" Residue "H ARG 716": "NH1" <-> "NH2" Residue "H ARG 733": "NH1" <-> "NH2" Residue "H ARG 736": "NH1" <-> "NH2" Residue "H ARG 774": "NH1" <-> "NH2" Residue "H ARG 821": "NH1" <-> "NH2" Residue "H ARG 845": "NH1" <-> "NH2" Residue "I ARG 240": "NH1" <-> "NH2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I ARG 265": "NH1" <-> "NH2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I ARG 367": "NH1" <-> "NH2" Residue "I ARG 376": "NH1" <-> "NH2" Residue "I ARG 418": "NH1" <-> "NH2" Residue "I ARG 439": "NH1" <-> "NH2" Residue "I ARG 461": "NH1" <-> "NH2" Residue "I ARG 477": "NH1" <-> "NH2" Residue "I ARG 486": "NH1" <-> "NH2" Residue "I ARG 487": "NH1" <-> "NH2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "I ARG 491": "NH1" <-> "NH2" Residue "I ARG 611": "NH1" <-> "NH2" Residue "I ARG 613": "NH1" <-> "NH2" Residue "I ARG 616": "NH1" <-> "NH2" Residue "I ARG 660": "NH1" <-> "NH2" Residue "I ARG 683": "NH1" <-> "NH2" Residue "I ARG 715": "NH1" <-> "NH2" Residue "I ARG 716": "NH1" <-> "NH2" Residue "I ARG 733": "NH1" <-> "NH2" Residue "I ARG 736": "NH1" <-> "NH2" Residue "I ARG 774": "NH1" <-> "NH2" Residue "I ARG 821": "NH1" <-> "NH2" Residue "I ARG 845": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 46702 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5286 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 21, 'TRANS': 637} Chain: "B" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 23.01, per 1000 atoms: 0.49 Number of scatterers: 46702 At special positions: 0 Unit cell: (196.56, 194.04, 198.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 307 16.00 O 8637 8.00 N 7918 7.00 C 29840 6.00 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: 19.78 Conformation dependent library (CDL) restraints added in 6.5 seconds 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11278 Finding SS restraints... Secondary structure from input PDB file: 413 helices and 9 sheets defined 80.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 195 through 226 Processing helix chain 'A' and resid 228 through 248 Processing helix chain 'A' and resid 252 through 267 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.775A pdb=" N ARG A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.644A pdb=" N GLU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.624A pdb=" N HIS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.694A pdb=" N VAL A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 448 " --> pdb=" O MET A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 455 through 468 removed outlier: 5.638A pdb=" N LYS A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 511 through 517 removed outlier: 4.142A pdb=" N GLN A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.965A pdb=" N ALA A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 561 through 572 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.975A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.525A pdb=" N LEU A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.542A pdb=" N LEU A 663 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 664 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 679 through 693 removed outlier: 4.090A pdb=" N THR A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 removed outlier: 3.857A pdb=" N LYS A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 4.183A pdb=" N ASN A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 772 through 776 Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 835 through 848 Processing helix chain 'B' and resid 195 through 226 Processing helix chain 'B' and resid 228 through 248 Processing helix chain 'B' and resid 252 through 267 Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 285 through 300 removed outlier: 3.767A pdb=" N ARG B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.686A pdb=" N HIS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.585A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.848A pdb=" N LEU B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.560A pdb=" N ASP B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 511 through 517 removed outlier: 4.079A pdb=" N GLN B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.953A pdb=" N ALA B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.541A pdb=" N GLY B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 577 through 584 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 595 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 644 through 648 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.163A pdb=" N SER B 664 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 666 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.572A pdb=" N ALA B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 733 Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.946A pdb=" N LEU B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 Processing helix chain 'B' and resid 783 through 795 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 820 through 826 Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 835 through 849 Processing helix chain 'C' and resid 195 through 226 Processing helix chain 'C' and resid 228 through 249 Processing helix chain 'C' and resid 252 through 267 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 285 through 300 removed outlier: 3.784A pdb=" N ARG C 289 " --> pdb=" O CYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.586A pdb=" N SER C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.654A pdb=" N HIS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 Processing helix chain 'C' and resid 390 through 400 removed outlier: 3.646A pdb=" N LYS C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 Processing helix chain 'C' and resid 414 through 430 Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 442 Processing helix chain 'C' and resid 442 through 453 removed outlier: 3.938A pdb=" N LEU C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 448 " --> pdb=" O MET C 444 " (cutoff:3.500A) Proline residue: C 449 - end of helix Processing helix chain 'C' and resid 455 through 468 removed outlier: 5.581A pdb=" N LYS C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 511 through 517 removed outlier: 4.089A pdb=" N GLN C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 529 removed outlier: 3.974A pdb=" N ALA C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 577 through 584 Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 595 through 602 Processing helix chain 'C' and resid 607 through 625 Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 649 through 656 Processing helix chain 'C' and resid 659 through 666 removed outlier: 3.543A pdb=" N LEU C 663 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER C 664 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 675 Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 719 through 733 Processing helix chain 'C' and resid 751 through 760 removed outlier: 3.836A pdb=" N LYS C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 776 Processing helix chain 'C' and resid 783 through 795 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.726A pdb=" N THR C 824 " --> pdb=" O ARG C 821 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 826 " --> pdb=" O ILE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 849 removed outlier: 3.954A pdb=" N MET C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 843 " --> pdb=" O CYS C 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 228 through 248 Processing helix chain 'D' and resid 252 through 267 Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.781A pdb=" N ARG D 289 " --> pdb=" O CYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.561A pdb=" N GLU D 354 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.633A pdb=" N HIS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.657A pdb=" N LYS D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 414 through 430 Processing helix chain 'D' and resid 434 through 442 Processing helix chain 'D' and resid 442 through 453 removed outlier: 3.956A pdb=" N LEU D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU D 448 " --> pdb=" O MET D 444 " (cutoff:3.500A) Proline residue: D 449 - end of helix Processing helix chain 'D' and resid 455 through 468 removed outlier: 3.690A pdb=" N ASP D 462 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS D 465 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 511 through 517 removed outlier: 4.087A pdb=" N GLN D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.863A pdb=" N ALA D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 546 Processing helix chain 'D' and resid 556 through 560 Processing helix chain 'D' and resid 561 through 572 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 577 through 584 Processing helix chain 'D' and resid 589 through 594 Processing helix chain 'D' and resid 595 through 602 Processing helix chain 'D' and resid 607 through 625 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 644 through 648 Processing helix chain 'D' and resid 649 through 656 Processing helix chain 'D' and resid 661 through 666 removed outlier: 3.985A pdb=" N SER D 664 " --> pdb=" O SER D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 679 through 693 removed outlier: 3.576A pdb=" N ALA D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 733 removed outlier: 3.711A pdb=" N ASN D 720 " --> pdb=" O ARG D 716 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN D 721 " --> pdb=" O SER D 717 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 759 Processing helix chain 'D' and resid 771 through 776 Processing helix chain 'D' and resid 783 through 795 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 820 through 826 Processing helix chain 'D' and resid 832 through 834 No H-bonds generated for 'chain 'D' and resid 832 through 834' Processing helix chain 'D' and resid 835 through 849 Processing helix chain 'E' and resid 195 through 225 Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 252 through 267 Processing helix chain 'E' and resid 268 through 279 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 285 through 300 removed outlier: 3.754A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 313 through 324 Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 345 through 354 removed outlier: 3.560A pdb=" N GLU E 354 " --> pdb=" O LEU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 368 removed outlier: 3.578A pdb=" N HIS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 388 Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.653A pdb=" N LYS E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 414 through 430 Processing helix chain 'E' and resid 434 through 442 Processing helix chain 'E' and resid 442 through 453 removed outlier: 3.851A pdb=" N LEU E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 448 " --> pdb=" O MET E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 455 through 468 removed outlier: 3.929A pdb=" N ASP E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS E 465 " --> pdb=" O ARG E 461 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 479 Processing helix chain 'E' and resid 480 through 483 Processing helix chain 'E' and resid 487 through 508 Processing helix chain 'E' and resid 511 through 517 removed outlier: 4.075A pdb=" N GLN E 515 " --> pdb=" O LEU E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 529 removed outlier: 3.970A pdb=" N ALA E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 546 Processing helix chain 'E' and resid 556 through 560 Processing helix chain 'E' and resid 561 through 572 Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 577 through 584 Processing helix chain 'E' and resid 587 through 594 Processing helix chain 'E' and resid 595 through 602 Processing helix chain 'E' and resid 607 through 625 Processing helix chain 'E' and resid 634 through 643 Processing helix chain 'E' and resid 644 through 648 Processing helix chain 'E' and resid 649 through 656 Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 667 through 674 Processing helix chain 'E' and resid 679 through 692 removed outlier: 3.557A pdb=" N ALA E 689 " --> pdb=" O LYS E 685 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE E 690 " --> pdb=" O LEU E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 732 Processing helix chain 'E' and resid 740 through 744 Processing helix chain 'E' and resid 750 through 759 removed outlier: 4.354A pdb=" N LEU E 754 " --> pdb=" O ASP E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 776 removed outlier: 4.071A pdb=" N ARG E 774 " --> pdb=" O SER E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 795 Processing helix chain 'E' and resid 812 through 816 Processing helix chain 'E' and resid 820 through 826 removed outlier: 3.618A pdb=" N TYR E 826 " --> pdb=" O ILE E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 849 Processing helix chain 'F' and resid 195 through 225 Processing helix chain 'F' and resid 228 through 248 Processing helix chain 'F' and resid 252 through 267 Processing helix chain 'F' and resid 268 through 279 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 285 through 300 removed outlier: 3.764A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 327 through 342 Processing helix chain 'F' and resid 345 through 354 removed outlier: 3.544A pdb=" N GLU F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 368 removed outlier: 3.708A pdb=" N HIS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 388 Processing helix chain 'F' and resid 390 through 400 removed outlier: 3.633A pdb=" N LYS F 400 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 412 Processing helix chain 'F' and resid 414 through 430 Processing helix chain 'F' and resid 431 through 433 No H-bonds generated for 'chain 'F' and resid 431 through 433' Processing helix chain 'F' and resid 434 through 440 Processing helix chain 'F' and resid 442 through 453 removed outlier: 3.889A pdb=" N GLU F 448 " --> pdb=" O MET F 444 " (cutoff:3.500A) Proline residue: F 449 - end of helix Processing helix chain 'F' and resid 455 through 468 removed outlier: 5.651A pdb=" N LYS F 465 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 479 Processing helix chain 'F' and resid 480 through 483 Processing helix chain 'F' and resid 487 through 508 Processing helix chain 'F' and resid 511 through 517 removed outlier: 4.095A pdb=" N GLN F 515 " --> pdb=" O LEU F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 529 removed outlier: 3.966A pdb=" N ALA F 522 " --> pdb=" O GLY F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 546 removed outlier: 3.522A pdb=" N GLY F 546 " --> pdb=" O LEU F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 560 Processing helix chain 'F' and resid 561 through 572 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 577 through 584 Processing helix chain 'F' and resid 587 through 594 Processing helix chain 'F' and resid 595 through 602 Processing helix chain 'F' and resid 607 through 625 Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 656 Processing helix chain 'F' and resid 661 through 666 removed outlier: 4.266A pdb=" N SER F 664 " --> pdb=" O SER F 661 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 666 " --> pdb=" O LEU F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 674 Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 715 through 733 removed outlier: 6.313A pdb=" N GLN F 721 " --> pdb=" O SER F 717 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU F 722 " --> pdb=" O THR F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 754 Processing helix chain 'F' and resid 754 through 760 removed outlier: 3.660A pdb=" N GLN F 758 " --> pdb=" O LEU F 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 776 Processing helix chain 'F' and resid 783 through 795 Processing helix chain 'F' and resid 812 through 816 Processing helix chain 'F' and resid 817 through 822 removed outlier: 4.582A pdb=" N MET F 822 " --> pdb=" O ASN F 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 826 Processing helix chain 'F' and resid 832 through 834 No H-bonds generated for 'chain 'F' and resid 832 through 834' Processing helix chain 'F' and resid 835 through 849 Processing helix chain 'G' and resid 195 through 226 Processing helix chain 'G' and resid 228 through 248 Processing helix chain 'G' and resid 252 through 267 Processing helix chain 'G' and resid 268 through 279 Processing helix chain 'G' and resid 280 through 284 Processing helix chain 'G' and resid 285 through 299 removed outlier: 3.691A pdb=" N ARG G 289 " --> pdb=" O CYS G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 313 through 324 Processing helix chain 'G' and resid 327 through 342 Processing helix chain 'G' and resid 345 through 354 removed outlier: 3.663A pdb=" N GLU G 354 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 removed outlier: 3.596A pdb=" N HIS G 360 " --> pdb=" O ASP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 388 Processing helix chain 'G' and resid 390 through 400 removed outlier: 3.649A pdb=" N LYS G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 411 Processing helix chain 'G' and resid 414 through 430 Processing helix chain 'G' and resid 431 through 433 No H-bonds generated for 'chain 'G' and resid 431 through 433' Processing helix chain 'G' and resid 434 through 442 Processing helix chain 'G' and resid 442 through 453 removed outlier: 3.819A pdb=" N LEU G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU G 448 " --> pdb=" O MET G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 455 through 468 removed outlier: 3.513A pdb=" N ARG G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 462 " --> pdb=" O THR G 458 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR G 466 " --> pdb=" O ASP G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 479 Processing helix chain 'G' and resid 480 through 483 Processing helix chain 'G' and resid 487 through 508 Processing helix chain 'G' and resid 511 through 517 removed outlier: 4.103A pdb=" N GLN G 515 " --> pdb=" O LEU G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 529 removed outlier: 3.969A pdb=" N ALA G 522 " --> pdb=" O GLY G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 546 removed outlier: 3.574A pdb=" N GLY G 546 " --> pdb=" O LEU G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 561 through 572 Processing helix chain 'G' and resid 574 through 576 No H-bonds generated for 'chain 'G' and resid 574 through 576' Processing helix chain 'G' and resid 577 through 584 Processing helix chain 'G' and resid 587 through 594 Processing helix chain 'G' and resid 595 through 602 Processing helix chain 'G' and resid 607 through 625 Processing helix chain 'G' and resid 634 through 643 Processing helix chain 'G' and resid 644 through 648 Processing helix chain 'G' and resid 649 through 656 Processing helix chain 'G' and resid 661 through 666 removed outlier: 4.116A pdb=" N SER G 664 " --> pdb=" O SER G 661 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 666 " --> pdb=" O LEU G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 674 Processing helix chain 'G' and resid 679 through 694 removed outlier: 4.113A pdb=" N LYS G 694 " --> pdb=" O PHE G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 719 through 731 Processing helix chain 'G' and resid 751 through 760 removed outlier: 4.369A pdb=" N ILE G 757 " --> pdb=" O LEU G 753 " (cutoff:3.500A) Processing helix chain 'G' and resid 772 through 776 Processing helix chain 'G' and resid 783 through 795 Processing helix chain 'G' and resid 812 through 816 Processing helix chain 'G' and resid 820 through 826 Processing helix chain 'G' and resid 832 through 834 No H-bonds generated for 'chain 'G' and resid 832 through 834' Processing helix chain 'G' and resid 835 through 849 Processing helix chain 'H' and resid 195 through 225 Processing helix chain 'H' and resid 228 through 248 Processing helix chain 'H' and resid 252 through 267 Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 285 through 300 removed outlier: 3.790A pdb=" N ARG H 289 " --> pdb=" O CYS H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 313 through 324 Processing helix chain 'H' and resid 327 through 342 Processing helix chain 'H' and resid 345 through 354 removed outlier: 3.600A pdb=" N GLU H 354 " --> pdb=" O LEU H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 368 removed outlier: 3.597A pdb=" N HIS H 360 " --> pdb=" O ASP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 388 Processing helix chain 'H' and resid 390 through 400 removed outlier: 3.629A pdb=" N LYS H 400 " --> pdb=" O LYS H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 412 Processing helix chain 'H' and resid 414 through 430 Processing helix chain 'H' and resid 431 through 433 No H-bonds generated for 'chain 'H' and resid 431 through 433' Processing helix chain 'H' and resid 434 through 441 Processing helix chain 'H' and resid 443 through 445 No H-bonds generated for 'chain 'H' and resid 443 through 445' Processing helix chain 'H' and resid 446 through 453 removed outlier: 3.670A pdb=" N VAL H 453 " --> pdb=" O PRO H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 468 removed outlier: 5.995A pdb=" N LYS H 465 " --> pdb=" O ARG H 461 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR H 466 " --> pdb=" O ASP H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 479 Processing helix chain 'H' and resid 480 through 483 Processing helix chain 'H' and resid 487 through 508 Processing helix chain 'H' and resid 511 through 517 removed outlier: 4.095A pdb=" N GLN H 515 " --> pdb=" O LEU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.985A pdb=" N ALA H 522 " --> pdb=" O GLY H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 546 removed outlier: 3.561A pdb=" N GLY H 546 " --> pdb=" O LEU H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 560 Processing helix chain 'H' and resid 561 through 572 Processing helix chain 'H' and resid 574 through 584 removed outlier: 3.593A pdb=" N VAL H 578 " --> pdb=" O PHE H 574 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU H 579 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS H 580 " --> pdb=" O GLU H 576 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 594 Processing helix chain 'H' and resid 595 through 602 Processing helix chain 'H' and resid 607 through 625 Processing helix chain 'H' and resid 634 through 643 Processing helix chain 'H' and resid 644 through 648 Processing helix chain 'H' and resid 649 through 656 Processing helix chain 'H' and resid 661 through 666 removed outlier: 4.125A pdb=" N SER H 664 " --> pdb=" O SER H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 675 Processing helix chain 'H' and resid 679 through 694 removed outlier: 4.158A pdb=" N LYS H 694 " --> pdb=" O PHE H 690 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 733 Processing helix chain 'H' and resid 750 through 760 removed outlier: 4.242A pdb=" N LEU H 754 " --> pdb=" O ASP H 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 772 through 776 Processing helix chain 'H' and resid 783 through 795 Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 820 through 826 Processing helix chain 'H' and resid 832 through 834 No H-bonds generated for 'chain 'H' and resid 832 through 834' Processing helix chain 'H' and resid 835 through 849 Processing helix chain 'I' and resid 195 through 226 Processing helix chain 'I' and resid 228 through 248 Processing helix chain 'I' and resid 252 through 267 Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 280 through 284 Processing helix chain 'I' and resid 285 through 299 removed outlier: 3.748A pdb=" N ARG I 289 " --> pdb=" O CYS I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 327 through 342 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 356 through 368 removed outlier: 3.777A pdb=" N HIS I 360 " --> pdb=" O ASP I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 388 Processing helix chain 'I' and resid 390 through 400 Processing helix chain 'I' and resid 401 through 412 Processing helix chain 'I' and resid 414 through 430 Processing helix chain 'I' and resid 431 through 433 No H-bonds generated for 'chain 'I' and resid 431 through 433' Processing helix chain 'I' and resid 434 through 442 Processing helix chain 'I' and resid 443 through 453 removed outlier: 4.130A pdb=" N GLU I 448 " --> pdb=" O MET I 444 " (cutoff:3.500A) Proline residue: I 449 - end of helix Processing helix chain 'I' and resid 455 through 468 removed outlier: 5.593A pdb=" N LYS I 465 " --> pdb=" O ARG I 461 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR I 466 " --> pdb=" O ASP I 462 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 468 " --> pdb=" O HIS I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 471 through 479 Processing helix chain 'I' and resid 480 through 483 Processing helix chain 'I' and resid 487 through 508 Processing helix chain 'I' and resid 511 through 517 removed outlier: 4.106A pdb=" N GLN I 515 " --> pdb=" O LEU I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 529 removed outlier: 3.978A pdb=" N ALA I 522 " --> pdb=" O GLY I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 546 removed outlier: 4.052A pdb=" N GLY I 546 " --> pdb=" O LEU I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 560 Processing helix chain 'I' and resid 561 through 572 Processing helix chain 'I' and resid 574 through 576 No H-bonds generated for 'chain 'I' and resid 574 through 576' Processing helix chain 'I' and resid 577 through 584 Processing helix chain 'I' and resid 589 through 594 removed outlier: 3.532A pdb=" N GLN I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 594 " --> pdb=" O LEU I 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 589 through 594' Processing helix chain 'I' and resid 595 through 602 Processing helix chain 'I' and resid 607 through 625 Processing helix chain 'I' and resid 634 through 643 Processing helix chain 'I' and resid 644 through 648 Processing helix chain 'I' and resid 649 through 656 Processing helix chain 'I' and resid 661 through 666 removed outlier: 4.131A pdb=" N SER I 664 " --> pdb=" O SER I 661 " (cutoff:3.500A) Processing helix chain 'I' and resid 667 through 674 Processing helix chain 'I' and resid 679 through 693 Processing helix chain 'I' and resid 719 through 733 Processing helix chain 'I' and resid 751 through 760 Processing helix chain 'I' and resid 772 through 776 Processing helix chain 'I' and resid 783 through 795 Processing helix chain 'I' and resid 812 through 816 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 832 through 834 No H-bonds generated for 'chain 'I' and resid 832 through 834' Processing helix chain 'I' and resid 835 through 849 Processing sheet with id=AA1, first strand: chain 'A' and resid 737 through 739 removed outlier: 6.361A pdb=" N VAL A 710 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 763 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE A 802 " --> pdb=" O PHE A 763 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 765 " --> pdb=" O ILE A 802 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 737 through 738 removed outlier: 3.747A pdb=" N PHE B 738 " --> pdb=" O VAL B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 737 through 739 removed outlier: 6.723A pdb=" N VAL C 710 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 829 " --> pdb=" O ILE C 799 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 737 through 739 removed outlier: 7.732A pdb=" N PHE D 738 " --> pdb=" O ILE D 708 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 710 " --> pdb=" O PHE D 738 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP D 709 " --> pdb=" O ALA D 760 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LYS D 761 " --> pdb=" O ASN D 798 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE D 800 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE D 763 " --> pdb=" O ILE D 800 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 802 " --> pdb=" O PHE D 763 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 765 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL D 829 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 737 through 739 removed outlier: 7.888A pdb=" N PHE E 738 " --> pdb=" O ILE E 708 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 710 " --> pdb=" O PHE E 738 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP E 709 " --> pdb=" O ALA E 760 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS E 761 " --> pdb=" O ASN E 798 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE E 800 " --> pdb=" O LYS E 761 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 763 " --> pdb=" O ILE E 800 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE E 802 " --> pdb=" O PHE E 763 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 765 " --> pdb=" O ILE E 802 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 737 through 739 removed outlier: 6.595A pdb=" N VAL F 710 " --> pdb=" O PHE F 738 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE F 763 " --> pdb=" O ILE F 800 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE F 802 " --> pdb=" O PHE F 763 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 765 " --> pdb=" O ILE F 802 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 737 through 739 removed outlier: 6.433A pdb=" N VAL G 710 " --> pdb=" O PHE G 738 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE G 763 " --> pdb=" O ASN G 798 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL G 829 " --> pdb=" O ILE G 799 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 737 through 739 removed outlier: 6.388A pdb=" N VAL H 710 " --> pdb=" O PHE H 738 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H 763 " --> pdb=" O ASN H 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 737 through 739 removed outlier: 5.912A pdb=" N VAL I 710 " --> pdb=" O PHE I 738 " (cutoff:3.500A) 2998 hydrogen bonds defined for protein. 8541 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: 21.60 Time building geometry restraints manager: 21.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.28: 7708 1.28 - 1.44: 12027 1.44 - 1.60: 27346 1.60 - 1.77: 13 1.77 - 1.93: 475 Bond restraints: 47569 Sorted by residual: bond pdb=" C TRP E 831 " pdb=" O TRP E 831 " ideal model delta sigma weight residual 1.234 1.143 0.092 1.22e-02 6.72e+03 5.63e+01 bond pdb=" C MET C 840 " pdb=" O MET C 840 " ideal model delta sigma weight residual 1.236 1.152 0.085 1.18e-02 7.18e+03 5.16e+01 bond pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 1.249 1.115 0.134 1.90e-02 2.77e+03 4.95e+01 bond pdb=" CE1 HIS G 360 " pdb=" NE2 HIS G 360 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" CG ASN A 679 " pdb=" OD1 ASN A 679 " ideal model delta sigma weight residual 1.231 1.116 0.115 1.90e-02 2.77e+03 3.67e+01 ... (remaining 47564 not shown) Histogram of bond angle deviations from ideal: 84.76 - 100.55: 99 100.55 - 116.34: 31559 116.34 - 132.14: 32488 132.14 - 147.93: 88 147.93 - 163.73: 1 Bond angle restraints: 64235 Sorted by residual: angle pdb=" CG GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE1 GLU F 501 " ideal model delta sigma weight residual 118.40 163.73 -45.33 2.30e+00 1.89e-01 3.88e+02 angle pdb=" CG GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 118.40 84.76 33.64 2.30e+00 1.89e-01 2.14e+02 angle pdb=" OE1 GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 122.90 93.02 29.88 2.40e+00 1.74e-01 1.55e+02 angle pdb=" C GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta sigma weight residual 110.31 133.00 -22.69 2.09e+00 2.29e-01 1.18e+02 angle pdb=" CA ASP C 455 " pdb=" CB ASP C 455 " pdb=" CG ASP C 455 " ideal model delta sigma weight residual 112.60 122.88 -10.28 1.00e+00 1.00e+00 1.06e+02 ... (remaining 64230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.34: 26550 18.34 - 36.69: 2177 36.69 - 55.03: 369 55.03 - 73.37: 59 73.37 - 91.72: 17 Dihedral angle restraints: 29172 sinusoidal: 11903 harmonic: 17269 Sorted by residual: dihedral pdb=" C GLN D 836 " pdb=" N GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta harmonic sigma weight residual -122.60 -155.34 32.74 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" N GLN D 836 " pdb=" C GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta harmonic sigma weight residual 122.80 147.71 -24.91 0 2.50e+00 1.60e-01 9.93e+01 dihedral pdb=" C ASP G 742 " pdb=" N ASP G 742 " pdb=" CA ASP G 742 " pdb=" CB ASP G 742 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 ... (remaining 29169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 6833 0.249 - 0.499: 484 0.499 - 0.748: 31 0.748 - 0.998: 3 0.998 - 1.247: 2 Chirality restraints: 7353 Sorted by residual: chirality pdb=" CA GLN D 836 " pdb=" N GLN D 836 " pdb=" C GLN D 836 " pdb=" CB GLN D 836 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.89e+01 chirality pdb=" CB VAL I 544 " pdb=" CA VAL I 544 " pdb=" CG1 VAL I 544 " pdb=" CG2 VAL I 544 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CB VAL A 565 " pdb=" CA VAL A 565 " pdb=" CG1 VAL A 565 " pdb=" CG2 VAL A 565 " both_signs ideal model delta sigma weight residual False -2.63 -1.68 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 7350 not shown) Planarity restraints: 8131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 714 " -0.184 2.00e-02 2.50e+03 1.03e-01 2.14e+02 pdb=" CG TYR I 714 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 714 " 0.140 2.00e-02 2.50e+03 pdb=" CD2 TYR I 714 " 0.108 2.00e-02 2.50e+03 pdb=" CE1 TYR I 714 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR I 714 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR I 714 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 714 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 463 " -0.134 2.00e-02 2.50e+03 7.15e-02 1.02e+02 pdb=" CG TYR B 463 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 463 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR B 463 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR B 463 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 463 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 463 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 463 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 567 " -0.129 2.00e-02 2.50e+03 6.94e-02 9.63e+01 pdb=" CG TYR A 567 " 0.126 2.00e-02 2.50e+03 pdb=" CD1 TYR A 567 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 567 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 567 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 567 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 567 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 567 " -0.037 2.00e-02 2.50e+03 ... (remaining 8128 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1277 2.73 - 3.27: 51689 3.27 - 3.82: 82051 3.82 - 4.36: 108332 4.36 - 4.90: 168531 Nonbonded interactions: 411880 Sorted by model distance: nonbonded pdb=" OE1 GLN E 688 " pdb=" OE1 GLU E 691 " model vdw 2.190 3.040 nonbonded pdb=" OG SER H 724 " pdb=" CE1 HIS I 833 " model vdw 2.193 3.260 nonbonded pdb=" OE1 GLN G 688 " pdb=" OE1 GLU G 691 " model vdw 2.329 3.040 nonbonded pdb=" OE2 GLU A 354 " pdb=" OD1 ASN I 310 " model vdw 2.355 3.040 nonbonded pdb=" O TYR C 835 " pdb=" OH TYR E 835 " model vdw 2.375 2.440 ... (remaining 411875 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' and (resid 194 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 695 or resid 707 through 849)) \ selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.950 Check model and map are aligned: 0.760 Set scattering table: 0.410 Process input model: 120.750 Find NCS groups from input model: 3.690 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.012 0.134 47569 Z= 0.757 Angle : 1.847 45.330 64235 Z= 1.197 Chirality : 0.139 1.247 7353 Planarity : 0.013 0.103 8131 Dihedral : 13.835 91.716 17894 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 4.32 % Favored : 93.78 % Cbeta Deviations : 1.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.09 % 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: -1.71 (0.10), residues: 5785 helix: -1.26 (0.07), residues: 4166 sheet: -2.16 (0.31), residues: 164 loop : 0.12 (0.18), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 587 time to evaluate : 6.052 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: 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: 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: 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: 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 outliers start: 98 outliers final: 20 residues processed: 666 average time/residue: 0.6713 time to fit residues: 708.3966 Evaluate side-chains 377 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 357 time to evaluate : 5.593 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4988 time to fit residues: 24.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 487 optimal weight: 4.9990 chunk 437 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 40.0000 chunk 295 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 452 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 523 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 555 GLN A 601 HIS B 566 GLN B 695 HIS ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 GLN C 707 GLN D 566 GLN E 468 GLN E 508 GLN E 509 ASN E 566 GLN F 468 GLN ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 ASN F 566 GLN F 652 GLN ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 GLN H 566 GLN I 509 ASN I 566 GLN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 47569 Z= 0.233 Angle : 0.672 13.737 64235 Z= 0.360 Chirality : 0.042 0.196 7353 Planarity : 0.004 0.038 8131 Dihedral : 5.397 30.190 6243 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 1.41 % Allowed : 9.09 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5785 helix: 0.72 (0.08), residues: 4255 sheet: -1.87 (0.34), residues: 167 loop : 0.78 (0.19), residues: 1363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 373 time to evaluate : 5.864 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 28 residues processed: 432 average time/residue: 0.6738 time to fit residues: 480.2427 Evaluate side-chains 335 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 6.024 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5550 time to fit residues: 34.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 291 optimal weight: 8.9990 chunk 162 optimal weight: 30.0000 chunk 436 optimal weight: 40.0000 chunk 356 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 524 optimal weight: 9.9990 chunk 567 optimal weight: 4.9990 chunk 467 optimal weight: 20.0000 chunk 520 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 421 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 ASN ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN E 231 ASN E 248 ASN E 497 HIS ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN G 508 GLN G 566 GLN G 652 GLN G 688 GLN G 695 HIS ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 GLN H 688 GLN I 196 ASN ** I 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47569 Z= 0.210 Angle : 0.624 9.843 64235 Z= 0.331 Chirality : 0.041 0.169 7353 Planarity : 0.004 0.065 8131 Dihedral : 5.033 27.901 6243 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.05 % Allowed : 10.09 % Favored : 88.86 % 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: 1.39 (0.11), residues: 5785 helix: 1.14 (0.08), residues: 4238 sheet: -1.93 (0.36), residues: 167 loop : 1.02 (0.20), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 346 time to evaluate : 5.652 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: 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: 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 outliers start: 54 outliers final: 21 residues processed: 395 average time/residue: 0.5877 time to fit residues: 391.7087 Evaluate side-chains 310 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 6.204 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4281 time to fit residues: 25.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 518 optimal weight: 5.9990 chunk 394 optimal weight: 0.2980 chunk 272 optimal weight: 40.0000 chunk 58 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 352 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 557 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 499 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 707 GLN ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN G 566 GLN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47569 Z= 0.197 Angle : 0.620 15.513 64235 Z= 0.323 Chirality : 0.041 0.265 7353 Planarity : 0.004 0.068 8131 Dihedral : 4.835 27.657 6243 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.91 % Allowed : 11.64 % Favored : 87.45 % 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: 1.49 (0.11), residues: 5785 helix: 1.19 (0.08), residues: 4246 sheet: -2.00 (0.37), residues: 169 loop : 1.16 (0.20), residues: 1370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 5.928 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 353 average time/residue: 0.5927 time to fit residues: 351.9690 Evaluate side-chains 321 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 299 time to evaluate : 5.393 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4860 time to fit residues: 26.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 464 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 415 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 475 optimal weight: 3.9990 chunk 385 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 284 optimal weight: 10.0000 chunk 500 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 360 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN C 721 GLN D 777 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN F 360 HIS ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 ASN F 566 GLN F 597 ASN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 ASN G 509 ASN G 566 GLN G 597 ASN H 281 ASN H 340 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 ASN H 566 GLN I 196 ASN I 340 ASN I 597 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 47569 Z= 0.258 Angle : 0.651 13.673 64235 Z= 0.342 Chirality : 0.041 0.222 7353 Planarity : 0.004 0.047 8131 Dihedral : 4.870 24.923 6243 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 13.08 % Favored : 85.92 % 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: 1.32 (0.11), residues: 5785 helix: 1.09 (0.08), residues: 4239 sheet: -1.99 (0.38), residues: 169 loop : 0.98 (0.19), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 6.315 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: 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: symmetry clash outliers start: 52 outliers final: 20 residues processed: 340 average time/residue: 0.5867 time to fit residues: 340.4309 Evaluate side-chains 295 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 6.610 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5081 time to fit residues: 26.0202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 187 optimal weight: 40.0000 chunk 502 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 558 optimal weight: 3.9990 chunk 463 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 184 optimal weight: 50.0000 chunk 293 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN F 248 ASN ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN G 566 GLN H 196 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 566 GLN I 340 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47569 Z= 0.228 Angle : 0.652 13.031 64235 Z= 0.338 Chirality : 0.041 0.222 7353 Planarity : 0.004 0.048 8131 Dihedral : 4.790 23.240 6243 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.79 % Allowed : 13.93 % Favored : 85.28 % 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 (0.11), residues: 5785 helix: 1.09 (0.08), residues: 4242 sheet: -2.03 (0.38), residues: 168 loop : 0.91 (0.19), residues: 1375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 6.156 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: 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 outliers start: 41 outliers final: 17 residues processed: 328 average time/residue: 0.5895 time to fit residues: 329.7702 Evaluate side-chains 292 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 275 time to evaluate : 6.332 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4340 time to fit residues: 22.0571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 538 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 318 optimal weight: 3.9990 chunk 407 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 469 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 556 optimal weight: 0.4980 chunk 348 optimal weight: 30.0000 chunk 339 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 HIS G 566 GLN H 196 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47569 Z= 0.197 Angle : 0.653 14.903 64235 Z= 0.333 Chirality : 0.041 0.245 7353 Planarity : 0.004 0.048 8131 Dihedral : 4.699 22.928 6243 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.56 % Allowed : 14.72 % Favored : 84.72 % 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: 1.40 (0.11), residues: 5785 helix: 1.15 (0.08), residues: 4229 sheet: -1.96 (0.39), residues: 168 loop : 1.01 (0.19), residues: 1388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 5.594 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: 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 outliers start: 29 outliers final: 11 residues processed: 324 average time/residue: 0.5829 time to fit residues: 320.8568 Evaluate side-chains 283 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 6.102 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4350 time to fit residues: 16.8103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 344 optimal weight: 8.9990 chunk 222 optimal weight: 40.0000 chunk 332 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 chunk 378 optimal weight: 40.0000 chunk 274 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 437 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 GLN H 196 ASN H 231 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 777 ASN I 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 47569 Z= 0.205 Angle : 0.675 14.554 64235 Z= 0.346 Chirality : 0.041 0.267 7353 Planarity : 0.004 0.051 8131 Dihedral : 4.681 22.815 6243 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.37 % Allowed : 15.44 % Favored : 84.19 % 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: 1.38 (0.12), residues: 5785 helix: 1.13 (0.08), residues: 4232 sheet: -1.91 (0.39), residues: 168 loop : 0.99 (0.19), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 283 time to evaluate : 5.904 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 298 average time/residue: 0.5816 time to fit residues: 295.8571 Evaluate side-chains 280 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 269 time to evaluate : 5.708 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4393 time to fit residues: 16.9929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 505 optimal weight: 6.9990 chunk 532 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 518 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 225 optimal weight: 0.4980 chunk 406 optimal weight: 8.9990 chunk 159 optimal weight: 30.0000 chunk 468 optimal weight: 9.9990 chunk 490 optimal weight: 0.2980 chunk 516 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 ASN ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 HIS ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 GLN H 196 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN I 597 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47569 Z= 0.187 Angle : 0.687 14.083 64235 Z= 0.349 Chirality : 0.042 0.348 7353 Planarity : 0.004 0.049 8131 Dihedral : 4.635 23.834 6243 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.65 % Rotamer: Outliers : 0.25 % Allowed : 15.83 % Favored : 83.92 % 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: 1.40 (0.12), residues: 5785 helix: 1.13 (0.08), residues: 4240 sheet: -1.88 (0.40), residues: 168 loop : 1.06 (0.20), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 6.575 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 298 average time/residue: 0.5734 time to fit residues: 294.8024 Evaluate side-chains 275 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 272 time to evaluate : 6.057 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5015 time to fit residues: 10.9957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 340 optimal weight: 7.9990 chunk 548 optimal weight: 1.9990 chunk 334 optimal weight: 0.0070 chunk 259 optimal weight: 8.9990 chunk 380 optimal weight: 6.9990 chunk 574 optimal weight: 20.0000 chunk 529 optimal weight: 30.0000 chunk 457 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 353 optimal weight: 5.9990 chunk 280 optimal weight: 40.0000 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47569 Z= 0.198 Angle : 0.708 14.485 64235 Z= 0.359 Chirality : 0.042 0.347 7353 Planarity : 0.004 0.049 8131 Dihedral : 4.638 25.943 6243 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 0.17 % Allowed : 16.12 % Favored : 83.71 % 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: 1.40 (0.12), residues: 5785 helix: 1.13 (0.08), residues: 4235 sheet: -1.91 (0.39), residues: 170 loop : 1.09 (0.20), residues: 1380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 279 time to evaluate : 5.919 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 283 average time/residue: 0.5953 time to fit residues: 287.6705 Evaluate side-chains 271 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 6.298 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5189 time to fit residues: 12.4011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 363 optimal weight: 4.9990 chunk 487 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 422 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 458 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 470 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN D 196 ASN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 619 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.100727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.083092 restraints weight = 401595.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.082434 restraints weight = 172188.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.082811 restraints weight = 93321.596| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47569 Z= 0.218 Angle : 0.725 14.012 64235 Z= 0.370 Chirality : 0.043 0.340 7353 Planarity : 0.004 0.059 8131 Dihedral : 4.679 26.803 6243 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 0.12 % Allowed : 16.29 % Favored : 83.59 % 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: 1.33 (0.12), residues: 5785 helix: 1.08 (0.08), residues: 4231 sheet: -1.95 (0.39), residues: 170 loop : 1.05 (0.20), residues: 1384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9052.78 seconds wall clock time: 168 minutes 32.32 seconds (10112.32 seconds total)